| anno_start anno_end anno_text entity_type sentence section | |
| 0 17 Crystal Structure evidence Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA TITLE | |
| 25 29 SPOC structure_element Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA TITLE | |
| 44 55 Arabidopsis taxonomy_domain Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA TITLE | |
| 56 75 Flowering Regulator protein_type Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA TITLE | |
| 76 79 FPA protein Crystal Structure of the SPOC Domain of the Arabidopsis Flowering Regulator FPA TITLE | |
| 4 15 Arabidopsis taxonomy_domain The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. ABSTRACT | |
| 24 27 FPA protein The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. ABSTRACT | |
| 107 122 FLOWERING LOCUS gene The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. ABSTRACT | |
| 124 127 FLC gene The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. ABSTRACT | |
| 129 142 antisense RNA chemical The Arabidopsis protein FPA controls flowering time by regulating the alternative 3′-end processing of the FLOWERING LOCUS (FLC) antisense RNA. ABSTRACT | |
| 0 3 FPA protein FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. ABSTRACT | |
| 19 29 split ends protein_type FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. ABSTRACT | |
| 31 35 SPEN protein_type FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. ABSTRACT | |
| 82 104 RNA recognition motifs structure_element FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. ABSTRACT | |
| 106 110 RRMs structure_element FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. ABSTRACT | |
| 118 154 SPEN paralog and ortholog C-terminal structure_element FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. ABSTRACT | |
| 156 160 SPOC structure_element FPA belongs to the split ends (SPEN) family of proteins, which contain N-terminal RNA recognition motifs (RRMs) and a SPEN paralog and ortholog C-terminal (SPOC) domain. ABSTRACT | |
| 4 8 SPOC structure_element The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. ABSTRACT | |
| 19 35 highly conserved protein_state The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. ABSTRACT | |
| 42 45 FPA protein The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. ABSTRACT | |
| 58 64 plants taxonomy_domain The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. ABSTRACT | |
| 112 116 SPEN protein_type The SPOC domain is highly conserved among FPA homologs in plants, but the conservation with the domain in other SPEN proteins is much lower. ABSTRACT | |
| 23 40 crystal structure evidence We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. ABSTRACT | |
| 44 64 Arabidopsis thaliana species We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. ABSTRACT | |
| 65 68 FPA protein We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. ABSTRACT | |
| 69 73 SPOC structure_element We have determined the crystal structure of Arabidopsis thaliana FPA SPOC domain at 2.7 Å resolution. ABSTRACT | |
| 12 21 structure evidence The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. ABSTRACT | |
| 48 52 SPOC structure_element The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. ABSTRACT | |
| 63 68 human species The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. ABSTRACT | |
| 69 108 SMRT/HDAC1 Associated Repressor Protein protein The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. ABSTRACT | |
| 110 115 SHARP protein The overall structure is similar to that of the SPOC domain in human SMRT/HDAC1 Associated Repressor Protein (SHARP), although there are also substantial conformational differences between them. ABSTRACT | |
| 0 32 Structural and sequence analyses experimental_method Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. ABSTRACT | |
| 44 57 surface patch site Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. ABSTRACT | |
| 66 75 conserved protein_state Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. ABSTRACT | |
| 82 87 plant taxonomy_domain Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. ABSTRACT | |
| 88 91 FPA protein Structural and sequence analyses identify a surface patch that is conserved among plant FPA homologs. ABSTRACT | |
| 0 9 Mutations experimental_method Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 34 47 surface patch site Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 64 67 FPA protein Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 106 110 SPOC structure_element Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 150 153 FPA protein Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 168 171 RNA chemical Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 213 216 FPA protein Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 217 221 SPOC structure_element Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 319 324 SHARP protein Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 325 329 SPOC structure_element Mutations of two residues in this surface patch did not disrupt FPA functions, suggesting that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation or the functions of the FPA SPOC domain cannot be disrupted by the combination of mutations, in contrast to observations with the SHARP SPOC domain. ABSTRACT | |
| 0 10 Eukaryotic taxonomy_domain Eukaryotic messenger RNAs (mRNAs) are made as precursors through transcription by RNA polymerase II (Pol II), and these primary transcripts undergo extensive processing, including 3′-end cleavage and polyadenylation. INTRO | |
| 11 25 messenger RNAs chemical Eukaryotic messenger RNAs (mRNAs) are made as precursors through transcription by RNA polymerase II (Pol II), and these primary transcripts undergo extensive processing, including 3′-end cleavage and polyadenylation. INTRO | |
| 27 32 mRNAs chemical Eukaryotic messenger RNAs (mRNAs) are made as precursors through transcription by RNA polymerase II (Pol II), and these primary transcripts undergo extensive processing, including 3′-end cleavage and polyadenylation. INTRO | |
| 82 99 RNA polymerase II complex_assembly Eukaryotic messenger RNAs (mRNAs) are made as precursors through transcription by RNA polymerase II (Pol II), and these primary transcripts undergo extensive processing, including 3′-end cleavage and polyadenylation. INTRO | |
| 101 107 Pol II complex_assembly Eukaryotic messenger RNAs (mRNAs) are made as precursors through transcription by RNA polymerase II (Pol II), and these primary transcripts undergo extensive processing, including 3′-end cleavage and polyadenylation. INTRO | |
| 103 113 eukaryotes taxonomy_domain In addition, alternative 3′-end cleavage and polyadenylation is an essential and ubiquitous process in eukaryotes. INTRO | |
| 14 24 split ends protein_type Recently, the split ends (SPEN) family of proteins was identified as RNA binding proteins that regulate alternative 3′-end cleavage and polyadenylation. INTRO | |
| 26 30 SPEN protein_type Recently, the split ends (SPEN) family of proteins was identified as RNA binding proteins that regulate alternative 3′-end cleavage and polyadenylation. INTRO | |
| 69 89 RNA binding proteins protein_type Recently, the split ends (SPEN) family of proteins was identified as RNA binding proteins that regulate alternative 3′-end cleavage and polyadenylation. INTRO | |
| 48 70 RNA recognition motifs structure_element They are characterized by possessing N-terminal RNA recognition motifs (RRMs) and a conserved SPEN paralog and ortholog C-terminal (SPOC) domain (Fig 1A). INTRO | |
| 72 76 RRMs structure_element They are characterized by possessing N-terminal RNA recognition motifs (RRMs) and a conserved SPEN paralog and ortholog C-terminal (SPOC) domain (Fig 1A). INTRO | |
| 84 93 conserved protein_state They are characterized by possessing N-terminal RNA recognition motifs (RRMs) and a conserved SPEN paralog and ortholog C-terminal (SPOC) domain (Fig 1A). INTRO | |
| 94 130 SPEN paralog and ortholog C-terminal structure_element They are characterized by possessing N-terminal RNA recognition motifs (RRMs) and a conserved SPEN paralog and ortholog C-terminal (SPOC) domain (Fig 1A). INTRO | |
| 132 136 SPOC structure_element They are characterized by possessing N-terminal RNA recognition motifs (RRMs) and a conserved SPEN paralog and ortholog C-terminal (SPOC) domain (Fig 1A). INTRO | |
| 4 8 SPOC structure_element The SPOC domain is believed to mediate protein-protein interactions and has diverse functions among SPEN family proteins, but the molecular mechanism of these functions is not well understood. INTRO | |
| 100 104 SPEN protein_type The SPOC domain is believed to mediate protein-protein interactions and has diverse functions among SPEN family proteins, but the molecular mechanism of these functions is not well understood. INTRO | |
| 0 21 Sequence conservation evidence Sequence conservation of SPOC domains. FIG | |
| 25 29 SPOC structure_element Sequence conservation of SPOC domains. FIG | |
| 23 34 A. thaliana species Domain organization of A. thaliana FPA. (B). FIG | |
| 35 38 FPA protein Domain organization of A. thaliana FPA. (B). FIG | |
| 0 18 Sequence alignment experimental_method Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 26 30 SPOC structure_element Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 42 62 Arabidopsis thaliana species Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 63 66 FPA protein Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 68 73 human species Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 74 79 RBM15 protein Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 81 91 Drosophila taxonomy_domain Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 92 96 SPEN protein_type Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 98 103 mouse taxonomy_domain Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 104 108 MINT protein Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 114 119 human species Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 120 125 SHARP protein Sequence alignment of the SPOC domains of Arabidopsis thaliana FPA, human RBM15, Drosophila SPEN, mouse MINT, and human SHARP. FIG | |
| 12 27 surface patch 1 site Residues in surface patch 1 are indicated with the orange dots, and those in surface patch 2 with the green dots. FIG | |
| 77 92 surface patch 2 site Residues in surface patch 1 are indicated with the orange dots, and those in surface patch 2 with the green dots. FIG | |
| 40 49 structure evidence The secondary structure elements in the structure of FPA SPOC are labeled. FIG | |
| 53 56 FPA protein The secondary structure elements in the structure of FPA SPOC are labeled. FIG | |
| 57 61 SPOC structure_element The secondary structure elements in the structure of FPA SPOC are labeled. FIG | |
| 18 36 strictly conserved protein_state Residues that are strictly conserved among the five proteins are shown in white with a red background, and those that are mostly conserved in red. FIG | |
| 122 138 mostly conserved protein_state Residues that are strictly conserved among the five proteins are shown in white with a red background, and those that are mostly conserved in red. FIG | |
| 0 3 FPA protein FPA, a SPEN family protein in Arabidopsis thaliana and other plants, was found to regulate the 3′-end alternative cleavage and polyadenylation of the antisense RNAs of FLOWERING LOCUS (FLC), a flowering repressor gene. INTRO | |
| 7 11 SPEN protein_type FPA, a SPEN family protein in Arabidopsis thaliana and other plants, was found to regulate the 3′-end alternative cleavage and polyadenylation of the antisense RNAs of FLOWERING LOCUS (FLC), a flowering repressor gene. INTRO | |
| 30 50 Arabidopsis thaliana species FPA, a SPEN family protein in Arabidopsis thaliana and other plants, was found to regulate the 3′-end alternative cleavage and polyadenylation of the antisense RNAs of FLOWERING LOCUS (FLC), a flowering repressor gene. INTRO | |
| 61 67 plants taxonomy_domain FPA, a SPEN family protein in Arabidopsis thaliana and other plants, was found to regulate the 3′-end alternative cleavage and polyadenylation of the antisense RNAs of FLOWERING LOCUS (FLC), a flowering repressor gene. INTRO | |
| 150 164 antisense RNAs chemical FPA, a SPEN family protein in Arabidopsis thaliana and other plants, was found to regulate the 3′-end alternative cleavage and polyadenylation of the antisense RNAs of FLOWERING LOCUS (FLC), a flowering repressor gene. INTRO | |
| 168 183 FLOWERING LOCUS gene FPA, a SPEN family protein in Arabidopsis thaliana and other plants, was found to regulate the 3′-end alternative cleavage and polyadenylation of the antisense RNAs of FLOWERING LOCUS (FLC), a flowering repressor gene. INTRO | |
| 185 188 FLC gene FPA, a SPEN family protein in Arabidopsis thaliana and other plants, was found to regulate the 3′-end alternative cleavage and polyadenylation of the antisense RNAs of FLOWERING LOCUS (FLC), a flowering repressor gene. INTRO | |
| 0 3 FPA protein FPA promotes the 3′-end processing of class I FLC antisense RNAs, which includes the proximal polyadenylation site. INTRO | |
| 46 49 FLC gene FPA promotes the 3′-end processing of class I FLC antisense RNAs, which includes the proximal polyadenylation site. INTRO | |
| 50 64 antisense RNAs chemical FPA promotes the 3′-end processing of class I FLC antisense RNAs, which includes the proximal polyadenylation site. INTRO | |
| 94 114 polyadenylation site site FPA promotes the 3′-end processing of class I FLC antisense RNAs, which includes the proximal polyadenylation site. INTRO | |
| 24 43 histone demethylase protein_type This is associated with histone demethylase activity and down-regulation of FLC transcription. INTRO | |
| 76 79 FLC gene This is associated with histone demethylase activity and down-regulation of FLC transcription. INTRO | |
| 11 15 SPOC structure_element Although a SPOC domain is found in all the SPEN family proteins, its sequence conservation is rather low. INTRO | |
| 43 47 SPEN protein_type Although a SPOC domain is found in all the SPEN family proteins, its sequence conservation is rather low. INTRO | |
| 47 51 SPOC structure_element For example, the sequence identity between the SPOC domains of A. thaliana FPA and human SMRT/HDAC1 Associated Repressor Protein (SHARP) is only 19% (Fig 1B). INTRO | |
| 63 74 A. thaliana species For example, the sequence identity between the SPOC domains of A. thaliana FPA and human SMRT/HDAC1 Associated Repressor Protein (SHARP) is only 19% (Fig 1B). INTRO | |
| 75 78 FPA protein For example, the sequence identity between the SPOC domains of A. thaliana FPA and human SMRT/HDAC1 Associated Repressor Protein (SHARP) is only 19% (Fig 1B). INTRO | |
| 83 88 human species For example, the sequence identity between the SPOC domains of A. thaliana FPA and human SMRT/HDAC1 Associated Repressor Protein (SHARP) is only 19% (Fig 1B). INTRO | |
| 89 128 SMRT/HDAC1 Associated Repressor Protein protein For example, the sequence identity between the SPOC domains of A. thaliana FPA and human SMRT/HDAC1 Associated Repressor Protein (SHARP) is only 19% (Fig 1B). INTRO | |
| 130 135 SHARP protein For example, the sequence identity between the SPOC domains of A. thaliana FPA and human SMRT/HDAC1 Associated Repressor Protein (SHARP) is only 19% (Fig 1B). INTRO | |
| 15 20 SHARP protein Currently, the SHARP SPOC domain is the only one with structural information. INTRO | |
| 21 25 SPOC structure_element Currently, the SHARP SPOC domain is the only one with structural information. INTRO | |
| 126 129 FPA protein As a first step toward understanding the molecular basis for the regulation of alternative 3′-end processing and flowering by FPA, we have determined the crystal structure of the SPOC domain of A. thaliana FPA at 2.7 Å resolution. INTRO | |
| 154 171 crystal structure evidence As a first step toward understanding the molecular basis for the regulation of alternative 3′-end processing and flowering by FPA, we have determined the crystal structure of the SPOC domain of A. thaliana FPA at 2.7 Å resolution. INTRO | |
| 179 183 SPOC structure_element As a first step toward understanding the molecular basis for the regulation of alternative 3′-end processing and flowering by FPA, we have determined the crystal structure of the SPOC domain of A. thaliana FPA at 2.7 Å resolution. INTRO | |
| 194 205 A. thaliana species As a first step toward understanding the molecular basis for the regulation of alternative 3′-end processing and flowering by FPA, we have determined the crystal structure of the SPOC domain of A. thaliana FPA at 2.7 Å resolution. INTRO | |
| 206 209 FPA protein As a first step toward understanding the molecular basis for the regulation of alternative 3′-end processing and flowering by FPA, we have determined the crystal structure of the SPOC domain of A. thaliana FPA at 2.7 Å resolution. INTRO | |
| 12 21 structure evidence The overall structure is similar to that of the SHARP SPOC domain, although there are also substantial conformational differences between them. INTRO | |
| 48 53 SHARP protein The overall structure is similar to that of the SHARP SPOC domain, although there are also substantial conformational differences between them. INTRO | |
| 54 58 SPOC structure_element The overall structure is similar to that of the SHARP SPOC domain, although there are also substantial conformational differences between them. INTRO | |
| 4 13 structure evidence The structure reveals a surface patch that is conserved among FPA homologs. INTRO | |
| 24 37 surface patch site The structure reveals a surface patch that is conserved among FPA homologs. INTRO | |
| 46 55 conserved protein_state The structure reveals a surface patch that is conserved among FPA homologs. INTRO | |
| 62 65 FPA protein The structure reveals a surface patch that is conserved among FPA homologs. INTRO | |
| 0 9 Structure evidence Structure of FPA SPOC domain RESULTS | |
| 13 16 FPA protein Structure of FPA SPOC domain RESULTS | |
| 17 21 SPOC structure_element Structure of FPA SPOC domain RESULTS | |
| 4 21 crystal structure evidence The crystal structure of the SPOC domain of A. thaliana FPA has been determined at 2.7 Å resolution using the selenomethionyl single-wavelength anomalous dispersion method. RESULTS | |
| 29 33 SPOC structure_element The crystal structure of the SPOC domain of A. thaliana FPA has been determined at 2.7 Å resolution using the selenomethionyl single-wavelength anomalous dispersion method. RESULTS | |
| 44 55 A. thaliana species The crystal structure of the SPOC domain of A. thaliana FPA has been determined at 2.7 Å resolution using the selenomethionyl single-wavelength anomalous dispersion method. RESULTS | |
| 56 59 FPA protein The crystal structure of the SPOC domain of A. thaliana FPA has been determined at 2.7 Å resolution using the selenomethionyl single-wavelength anomalous dispersion method. RESULTS | |
| 110 171 selenomethionyl single-wavelength anomalous dispersion method experimental_method The crystal structure of the SPOC domain of A. thaliana FPA has been determined at 2.7 Å resolution using the selenomethionyl single-wavelength anomalous dispersion method. RESULTS | |
| 44 51 433–565 residue_range The expression construct contained residues 433–565 of FPA, but only residues 439–460 and 465–565 are ordered in the crystal. RESULTS | |
| 55 58 FPA protein The expression construct contained residues 433–565 of FPA, but only residues 439–460 and 465–565 are ordered in the crystal. RESULTS | |
| 78 85 439–460 residue_range The expression construct contained residues 433–565 of FPA, but only residues 439–460 and 465–565 are ordered in the crystal. RESULTS | |
| 90 97 465–565 residue_range The expression construct contained residues 433–565 of FPA, but only residues 439–460 and 465–565 are ordered in the crystal. RESULTS | |
| 117 124 crystal evidence The expression construct contained residues 433–565 of FPA, but only residues 439–460 and 465–565 are ordered in the crystal. RESULTS | |
| 4 16 atomic model evidence The atomic model has good agreement with the X-ray diffraction data and the expected bond lengths, bond angles and other geometric parameters (Table 1). RESULTS | |
| 45 67 X-ray diffraction data evidence The atomic model has good agreement with the X-ray diffraction data and the expected bond lengths, bond angles and other geometric parameters (Table 1). RESULTS | |
| 59 76 Ramachandran plot evidence All the residues are located in the favored regions of the Ramachandran plot (data not shown). RESULTS | |
| 4 13 structure evidence The structure has been deposited in the Protein Data Bank, with accession code 5KXF. RESULTS | |
| 159 167 R factor evidence "Resolution range (Å)1 50–2.7 (2.8–2.7) Number of observations 78,008 Rmerge (%) 10.5 (45.3) I/σI 24.1 (6.3) Redundancy Completeness (%) 100 (100) R factor (%) 19.2 (25.0) Free R factor (%) 25.4 (35.4) Rms deviation in bond lengths (Å) 0.017 Rms deviation in bond angles (°) 1.9 " TABLE | |
| 186 199 Free R factor evidence "Resolution range (Å)1 50–2.7 (2.8–2.7) Number of observations 78,008 Rmerge (%) 10.5 (45.3) I/σI 24.1 (6.3) Redundancy Completeness (%) 100 (100) R factor (%) 19.2 (25.0) Free R factor (%) 25.4 (35.4) Rms deviation in bond lengths (Å) 0.017 Rms deviation in bond angles (°) 1.9 " TABLE | |
| 4 21 crystal structure evidence The crystal structure of the FPA SPOC domain contains a seven-stranded, mostly anti-parallel β-barrel (β1-β7) and three helices (αA-αC) (Fig 2A). RESULTS | |
| 29 32 FPA protein The crystal structure of the FPA SPOC domain contains a seven-stranded, mostly anti-parallel β-barrel (β1-β7) and three helices (αA-αC) (Fig 2A). RESULTS | |
| 33 37 SPOC structure_element The crystal structure of the FPA SPOC domain contains a seven-stranded, mostly anti-parallel β-barrel (β1-β7) and three helices (αA-αC) (Fig 2A). RESULTS | |
| 56 101 seven-stranded, mostly anti-parallel β-barrel structure_element The crystal structure of the FPA SPOC domain contains a seven-stranded, mostly anti-parallel β-barrel (β1-β7) and three helices (αA-αC) (Fig 2A). RESULTS | |
| 103 108 β1-β7 structure_element The crystal structure of the FPA SPOC domain contains a seven-stranded, mostly anti-parallel β-barrel (β1-β7) and three helices (αA-αC) (Fig 2A). RESULTS | |
| 120 127 helices structure_element The crystal structure of the FPA SPOC domain contains a seven-stranded, mostly anti-parallel β-barrel (β1-β7) and three helices (αA-αC) (Fig 2A). RESULTS | |
| 129 134 αA-αC structure_element The crystal structure of the FPA SPOC domain contains a seven-stranded, mostly anti-parallel β-barrel (β1-β7) and three helices (αA-αC) (Fig 2A). RESULTS | |
| 28 35 strands structure_element Only two of the neighboring strands, β1 and β3, are parallel to each other. RESULTS | |
| 37 39 β1 structure_element Only two of the neighboring strands, β1 and β3, are parallel to each other. RESULTS | |
| 44 46 β3 structure_element Only two of the neighboring strands, β1 and β3, are parallel to each other. RESULTS | |
| 0 5 Helix structure_element Helix αB covers one end of the barrel, while helices αA and αC are located next to each other at one side of the barrel (Fig 2B). RESULTS | |
| 6 8 αB structure_element Helix αB covers one end of the barrel, while helices αA and αC are located next to each other at one side of the barrel (Fig 2B). RESULTS | |
| 31 37 barrel structure_element Helix αB covers one end of the barrel, while helices αA and αC are located next to each other at one side of the barrel (Fig 2B). RESULTS | |
| 45 52 helices structure_element Helix αB covers one end of the barrel, while helices αA and αC are located next to each other at one side of the barrel (Fig 2B). RESULTS | |
| 53 55 αA structure_element Helix αB covers one end of the barrel, while helices αA and αC are located next to each other at one side of the barrel (Fig 2B). RESULTS | |
| 60 62 αC structure_element Helix αB covers one end of the barrel, while helices αA and αC are located next to each other at one side of the barrel (Fig 2B). RESULTS | |
| 113 119 barrel structure_element Helix αB covers one end of the barrel, while helices αA and αC are located next to each other at one side of the barrel (Fig 2B). RESULTS | |
| 21 29 β-barrel structure_element The other end of the β-barrel is covered by the loop connecting strands β2 and β3, which contains the disordered 461–464 segment. RESULTS | |
| 48 52 loop structure_element The other end of the β-barrel is covered by the loop connecting strands β2 and β3, which contains the disordered 461–464 segment. RESULTS | |
| 64 71 strands structure_element The other end of the β-barrel is covered by the loop connecting strands β2 and β3, which contains the disordered 461–464 segment. RESULTS | |
| 72 74 β2 structure_element The other end of the β-barrel is covered by the loop connecting strands β2 and β3, which contains the disordered 461–464 segment. RESULTS | |
| 79 81 β3 structure_element The other end of the β-barrel is covered by the loop connecting strands β2 and β3, which contains the disordered 461–464 segment. RESULTS | |
| 102 112 disordered protein_state The other end of the β-barrel is covered by the loop connecting strands β2 and β3, which contains the disordered 461–464 segment. RESULTS | |
| 113 120 461–464 residue_range The other end of the β-barrel is covered by the loop connecting strands β2 and β3, which contains the disordered 461–464 segment. RESULTS | |
| 18 24 barrel structure_element The center of the barrel is filled with hydrophobic side chains and is not accessible to the solvent. RESULTS | |
| 0 17 Crystal structure evidence Crystal structure of the SPOC domain of A. thaliana FPA. FIG | |
| 25 29 SPOC structure_element Crystal structure of the SPOC domain of A. thaliana FPA. FIG | |
| 40 51 A. thaliana species Crystal structure of the SPOC domain of A. thaliana FPA. FIG | |
| 52 55 FPA protein Crystal structure of the SPOC domain of A. thaliana FPA. FIG | |
| 25 34 structure evidence Schematic drawing of the structure of FPA SPOC domain, colored from blue at the N terminus to red at the C terminus. FIG | |
| 38 41 FPA protein Schematic drawing of the structure of FPA SPOC domain, colored from blue at the N terminus to red at the C terminus. FIG | |
| 42 46 SPOC structure_element Schematic drawing of the structure of FPA SPOC domain, colored from blue at the N terminus to red at the C terminus. FIG | |
| 33 41 β-barrel structure_element The view is from the side of the β-barrel. FIG | |
| 4 14 disordered protein_state The disordered segment (residues 460–465) is indicated with the dotted line. FIG | |
| 33 40 460–465 residue_range The disordered segment (residues 460–465) is indicated with the dotted line. FIG | |
| 0 9 Structure evidence Structure of the FPA SPOC domain, viewed from the end of the β-barrel, after 90° rotation around the horizontal axis from panel A. All structure figures were produced with PyMOL (www.pymol.org). FIG | |
| 17 20 FPA protein Structure of the FPA SPOC domain, viewed from the end of the β-barrel, after 90° rotation around the horizontal axis from panel A. All structure figures were produced with PyMOL (www.pymol.org). FIG | |
| 21 25 SPOC structure_element Structure of the FPA SPOC domain, viewed from the end of the β-barrel, after 90° rotation around the horizontal axis from panel A. All structure figures were produced with PyMOL (www.pymol.org). FIG | |
| 61 69 β-barrel structure_element Structure of the FPA SPOC domain, viewed from the end of the β-barrel, after 90° rotation around the horizontal axis from panel A. All structure figures were produced with PyMOL (www.pymol.org). FIG | |
| 0 34 Comparisons to structural homologs experimental_method Comparisons to structural homologs of the SPOC domain RESULTS | |
| 42 46 SPOC structure_element Comparisons to structural homologs of the SPOC domain RESULTS | |
| 37 40 FPA protein Only five structural homologs of the FPA SPOC domain were found in the Protein Data Bank with the DaliLite server, suggesting that the SPOC domain structure is relatively unique. RESULTS | |
| 41 45 SPOC structure_element Only five structural homologs of the FPA SPOC domain were found in the Protein Data Bank with the DaliLite server, suggesting that the SPOC domain structure is relatively unique. RESULTS | |
| 98 113 DaliLite server experimental_method Only five structural homologs of the FPA SPOC domain were found in the Protein Data Bank with the DaliLite server, suggesting that the SPOC domain structure is relatively unique. RESULTS | |
| 135 139 SPOC structure_element Only five structural homologs of the FPA SPOC domain were found in the Protein Data Bank with the DaliLite server, suggesting that the SPOC domain structure is relatively unique. RESULTS | |
| 147 156 structure evidence Only five structural homologs of the FPA SPOC domain were found in the Protein Data Bank with the DaliLite server, suggesting that the SPOC domain structure is relatively unique. RESULTS | |
| 19 23 SPOC structure_element The top hit is the SPOC domain of human SHARP (Fig 3A), with a Z score of 12.3. RESULTS | |
| 34 39 human species The top hit is the SPOC domain of human SHARP (Fig 3A), with a Z score of 12.3. RESULTS | |
| 40 45 SHARP protein The top hit is the SPOC domain of human SHARP (Fig 3A), with a Z score of 12.3. RESULTS | |
| 63 70 Z score evidence The top hit is the SPOC domain of human SHARP (Fig 3A), with a Z score of 12.3. RESULTS | |
| 47 55 β-barrel structure_element The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 79 83 Ku70 protein The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 88 92 Ku80 protein The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 94 101 Z score evidence The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 134 154 chromodomain protein protein_type The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 155 159 Chp1 protein The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 161 168 Z score evidence The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 193 221 activator interacting domain structure_element The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 223 227 ACID structure_element The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 236 241 Med25 protein The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 275 282 Z score evidence The other four structural homologs include the β-barrel domain of the proteins Ku70 and Ku80 (Z score 11.4) (Fig 3B), a domain in the chromodomain protein Chp1 (Z score 10.8) (Fig 3C), and the activator interacting domain (ACID) of the Med25 subunit of the Mediator complex (Z score 8.5) (Fig 3D). RESULTS | |
| 34 41 Z score evidence The next structural homolog has a Z score of 3.0. RESULTS | |
| 27 30 FPA protein Structural homologs of the FPA SPOC domain. FIG | |
| 31 35 SPOC structure_element Structural homologs of the FPA SPOC domain. FIG | |
| 0 7 Overlay experimental_method Overlay of the structures of the FPA SPOC domain (cyan) and the SHARP SPOC domain (gray). FIG | |
| 15 25 structures evidence Overlay of the structures of the FPA SPOC domain (cyan) and the SHARP SPOC domain (gray). FIG | |
| 33 36 FPA protein Overlay of the structures of the FPA SPOC domain (cyan) and the SHARP SPOC domain (gray). FIG | |
| 37 41 SPOC structure_element Overlay of the structures of the FPA SPOC domain (cyan) and the SHARP SPOC domain (gray). FIG | |
| 64 69 SHARP protein Overlay of the structures of the FPA SPOC domain (cyan) and the SHARP SPOC domain (gray). FIG | |
| 70 74 SPOC structure_element Overlay of the structures of the FPA SPOC domain (cyan) and the SHARP SPOC domain (gray). FIG | |
| 24 45 doubly-phosphorylated protein_state The bound position of a doubly-phosphorylated peptide from SMRT is shown in magenta. FIG | |
| 46 53 peptide chemical The bound position of a doubly-phosphorylated peptide from SMRT is shown in magenta. FIG | |
| 59 63 SMRT protein The bound position of a doubly-phosphorylated peptide from SMRT is shown in magenta. FIG | |
| 0 7 Overlay experimental_method Overlay of the structures of the FPA SPOC domain (cyan) and the Ku70 β-barrel domain (gray). FIG | |
| 15 25 structures evidence Overlay of the structures of the FPA SPOC domain (cyan) and the Ku70 β-barrel domain (gray). FIG | |
| 33 36 FPA protein Overlay of the structures of the FPA SPOC domain (cyan) and the Ku70 β-barrel domain (gray). FIG | |
| 37 41 SPOC structure_element Overlay of the structures of the FPA SPOC domain (cyan) and the Ku70 β-barrel domain (gray). FIG | |
| 64 68 Ku70 protein Overlay of the structures of the FPA SPOC domain (cyan) and the Ku70 β-barrel domain (gray). FIG | |
| 69 77 β-barrel structure_element Overlay of the structures of the FPA SPOC domain (cyan) and the Ku70 β-barrel domain (gray). FIG | |
| 0 4 Ku80 protein Ku80 contains a homologous domain (green), which forms a hetero-dimer with that in Ku70. FIG | |
| 57 69 hetero-dimer oligomeric_state Ku80 contains a homologous domain (green), which forms a hetero-dimer with that in Ku70. FIG | |
| 83 87 Ku70 protein Ku80 contains a homologous domain (green), which forms a hetero-dimer with that in Ku70. FIG | |
| 71 76 dsDNA chemical The two domains, and inserted segments on them, mediate the binding of dsDNA (orange). FIG | |
| 67 75 β-barrel structure_element The red rectangle highlights the region of contact between the two β-barrel domains. FIG | |
| 0 7 Overlay experimental_method Overlay of the structures of the FPA SPOC domain (cyan) and the homologous domain in Chp1 (gray). FIG | |
| 15 25 structures evidence Overlay of the structures of the FPA SPOC domain (cyan) and the homologous domain in Chp1 (gray). FIG | |
| 33 36 FPA protein Overlay of the structures of the FPA SPOC domain (cyan) and the homologous domain in Chp1 (gray). FIG | |
| 37 41 SPOC structure_element Overlay of the structures of the FPA SPOC domain (cyan) and the homologous domain in Chp1 (gray). FIG | |
| 85 89 Chp1 protein Overlay of the structures of the FPA SPOC domain (cyan) and the homologous domain in Chp1 (gray). FIG | |
| 23 27 Chp1 protein The binding partner of Chp1, Tas3, is shown in green. FIG | |
| 29 33 Tas3 protein The binding partner of Chp1, Tas3, is shown in green. FIG | |
| 57 69 binding site site The red rectangle indicates the region equivalent to the binding site of the SMART phosphopeptide in SHARP SPOC domain, where a loop of Tas3 is also located. (D). FIG | |
| 77 82 SMART protein The red rectangle indicates the region equivalent to the binding site of the SMART phosphopeptide in SHARP SPOC domain, where a loop of Tas3 is also located. (D). FIG | |
| 83 97 phosphopeptide ptm The red rectangle indicates the region equivalent to the binding site of the SMART phosphopeptide in SHARP SPOC domain, where a loop of Tas3 is also located. (D). FIG | |
| 101 106 SHARP protein The red rectangle indicates the region equivalent to the binding site of the SMART phosphopeptide in SHARP SPOC domain, where a loop of Tas3 is also located. (D). FIG | |
| 107 111 SPOC structure_element The red rectangle indicates the region equivalent to the binding site of the SMART phosphopeptide in SHARP SPOC domain, where a loop of Tas3 is also located. (D). FIG | |
| 128 132 loop structure_element The red rectangle indicates the region equivalent to the binding site of the SMART phosphopeptide in SHARP SPOC domain, where a loop of Tas3 is also located. (D). FIG | |
| 136 140 Tas3 protein The red rectangle indicates the region equivalent to the binding site of the SMART phosphopeptide in SHARP SPOC domain, where a loop of Tas3 is also located. (D). FIG | |
| 0 7 Overlay experimental_method Overlay of the structures of the FPA SPOC domain (cyan) and the Med25 ACID (gray). FIG | |
| 15 25 structures evidence Overlay of the structures of the FPA SPOC domain (cyan) and the Med25 ACID (gray). FIG | |
| 33 36 FPA protein Overlay of the structures of the FPA SPOC domain (cyan) and the Med25 ACID (gray). FIG | |
| 37 41 SPOC structure_element Overlay of the structures of the FPA SPOC domain (cyan) and the Med25 ACID (gray). FIG | |
| 64 69 Med25 protein Overlay of the structures of the FPA SPOC domain (cyan) and the Med25 ACID (gray). FIG | |
| 70 74 ACID structure_element Overlay of the structures of the FPA SPOC domain (cyan) and the Med25 ACID (gray). FIG | |
| 0 5 SHARP protein SHARP is a transcriptional co-repressor in the nuclear receptor and Notch/RBP-Jκ signaling pathways. RESULTS | |
| 11 39 transcriptional co-repressor protein_type SHARP is a transcriptional co-repressor in the nuclear receptor and Notch/RBP-Jκ signaling pathways. RESULTS | |
| 47 63 nuclear receptor protein_type SHARP is a transcriptional co-repressor in the nuclear receptor and Notch/RBP-Jκ signaling pathways. RESULTS | |
| 68 73 Notch protein SHARP is a transcriptional co-repressor in the nuclear receptor and Notch/RBP-Jκ signaling pathways. RESULTS | |
| 74 80 RBP-Jκ protein SHARP is a transcriptional co-repressor in the nuclear receptor and Notch/RBP-Jκ signaling pathways. RESULTS | |
| 4 8 SPOC structure_element The SPOC domain of SHARP interacts directly with silencing mediator for retinoid and thyroid receptor (SMRT), nuclear receptor co-repressor (N-CoR), HDAC, and other components to represses transcription. RESULTS | |
| 19 24 SHARP protein The SPOC domain of SHARP interacts directly with silencing mediator for retinoid and thyroid receptor (SMRT), nuclear receptor co-repressor (N-CoR), HDAC, and other components to represses transcription. RESULTS | |
| 49 101 silencing mediator for retinoid and thyroid receptor protein The SPOC domain of SHARP interacts directly with silencing mediator for retinoid and thyroid receptor (SMRT), nuclear receptor co-repressor (N-CoR), HDAC, and other components to represses transcription. RESULTS | |
| 103 107 SMRT protein The SPOC domain of SHARP interacts directly with silencing mediator for retinoid and thyroid receptor (SMRT), nuclear receptor co-repressor (N-CoR), HDAC, and other components to represses transcription. RESULTS | |
| 110 139 nuclear receptor co-repressor protein_type The SPOC domain of SHARP interacts directly with silencing mediator for retinoid and thyroid receptor (SMRT), nuclear receptor co-repressor (N-CoR), HDAC, and other components to represses transcription. RESULTS | |
| 141 146 N-CoR protein_type The SPOC domain of SHARP interacts directly with silencing mediator for retinoid and thyroid receptor (SMRT), nuclear receptor co-repressor (N-CoR), HDAC, and other components to represses transcription. RESULTS | |
| 149 153 HDAC protein The SPOC domain of SHARP interacts directly with silencing mediator for retinoid and thyroid receptor (SMRT), nuclear receptor co-repressor (N-CoR), HDAC, and other components to represses transcription. RESULTS | |
| 18 27 structure evidence While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 35 38 FPA protein While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 39 43 SPOC structure_element While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 77 82 SHARP protein While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 83 87 SPOC structure_element While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 155 164 β-strands structure_element While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 173 180 helices structure_element While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 198 203 loops structure_element While the overall structure of the FPA SPOC domain is similar to that of the SHARP SPOC domain, there are noticeable differences in the positioning of the β-strands and the helices, and most of the loops have substantially different conformations as well (Fig 3A). RESULTS | |
| 17 22 SHARP protein In addition, the SHARP SPOC domain has three extra helices. RESULTS | |
| 23 27 SPOC structure_element In addition, the SHARP SPOC domain has three extra helices. RESULTS | |
| 51 58 helices structure_element In addition, the SHARP SPOC domain has three extra helices. RESULTS | |
| 40 48 β-barrel structure_element One of them covers the other end of the β-barrel, and the other two shield an additional surface of the side of the β-barrel from solvent. RESULTS | |
| 116 124 β-barrel structure_element One of them covers the other end of the β-barrel, and the other two shield an additional surface of the side of the β-barrel from solvent. RESULTS | |
| 2 23 doubly-phosphorylated protein_state A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 24 31 peptide chemical A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 37 41 SMRT protein A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 45 53 bound to protein_state A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 70 76 barrel structure_element A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 83 90 strands structure_element A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 91 93 β1 structure_element A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 98 100 β3 structure_element A doubly-phosphorylated peptide from SMRT is bound to the side of the barrel, near strands β1 and β3 (Fig 3A). RESULTS | |
| 54 57 FPA protein Such a binding mode probably would not be possible in FPA, as the peptide would clash with the β1-β2 loop. RESULTS | |
| 66 73 peptide chemical Such a binding mode probably would not be possible in FPA, as the peptide would clash with the β1-β2 loop. RESULTS | |
| 95 105 β1-β2 loop structure_element Such a binding mode probably would not be possible in FPA, as the peptide would clash with the β1-β2 loop. RESULTS | |
| 4 13 Ku70-Ku80 complex_assembly The Ku70-Ku80 hetero-dimer is involved in DNA double-strand break repair and the β-barrel domain contributes to DNA binding. RESULTS | |
| 14 26 hetero-dimer oligomeric_state The Ku70-Ku80 hetero-dimer is involved in DNA double-strand break repair and the β-barrel domain contributes to DNA binding. RESULTS | |
| 81 89 β-barrel structure_element The Ku70-Ku80 hetero-dimer is involved in DNA double-strand break repair and the β-barrel domain contributes to DNA binding. RESULTS | |
| 112 115 DNA chemical The Ku70-Ku80 hetero-dimer is involved in DNA double-strand break repair and the β-barrel domain contributes to DNA binding. RESULTS | |
| 13 21 β-barrel structure_element In fact, the β-barrel domains of Ku70 and Ku80 form a hetero-dimer, primarily through interactions between the loops connecting the third and fourth strands of the barrel (Fig 3B). RESULTS | |
| 33 37 Ku70 protein In fact, the β-barrel domains of Ku70 and Ku80 form a hetero-dimer, primarily through interactions between the loops connecting the third and fourth strands of the barrel (Fig 3B). RESULTS | |
| 42 46 Ku80 protein In fact, the β-barrel domains of Ku70 and Ku80 form a hetero-dimer, primarily through interactions between the loops connecting the third and fourth strands of the barrel (Fig 3B). RESULTS | |
| 54 66 hetero-dimer oligomeric_state In fact, the β-barrel domains of Ku70 and Ku80 form a hetero-dimer, primarily through interactions between the loops connecting the third and fourth strands of the barrel (Fig 3B). RESULTS | |
| 111 116 loops structure_element In fact, the β-barrel domains of Ku70 and Ku80 form a hetero-dimer, primarily through interactions between the loops connecting the third and fourth strands of the barrel (Fig 3B). RESULTS | |
| 132 156 third and fourth strands structure_element In fact, the β-barrel domains of Ku70 and Ku80 form a hetero-dimer, primarily through interactions between the loops connecting the third and fourth strands of the barrel (Fig 3B). RESULTS | |
| 164 170 barrel structure_element In fact, the β-barrel domains of Ku70 and Ku80 form a hetero-dimer, primarily through interactions between the loops connecting the third and fourth strands of the barrel (Fig 3B). RESULTS | |
| 25 34 β-barrels structure_element The open ends of the two β-barrels face the DNA binding sites, and contact the phosphodiester backbone of the dsDNA. RESULTS | |
| 44 61 DNA binding sites site The open ends of the two β-barrels face the DNA binding sites, and contact the phosphodiester backbone of the dsDNA. RESULTS | |
| 110 115 dsDNA chemical The open ends of the two β-barrels face the DNA binding sites, and contact the phosphodiester backbone of the dsDNA. RESULTS | |
| 15 26 long insert structure_element In addition, a long insert connecting strands β2 and β3 in the two domains form an arch-like structure, encircling the dsDNA. RESULTS | |
| 38 45 strands structure_element In addition, a long insert connecting strands β2 and β3 in the two domains form an arch-like structure, encircling the dsDNA. RESULTS | |
| 46 48 β2 structure_element In addition, a long insert connecting strands β2 and β3 in the two domains form an arch-like structure, encircling the dsDNA. RESULTS | |
| 53 55 β3 structure_element In addition, a long insert connecting strands β2 and β3 in the two domains form an arch-like structure, encircling the dsDNA. RESULTS | |
| 83 102 arch-like structure structure_element In addition, a long insert connecting strands β2 and β3 in the two domains form an arch-like structure, encircling the dsDNA. RESULTS | |
| 119 124 dsDNA chemical In addition, a long insert connecting strands β2 and β3 in the two domains form an arch-like structure, encircling the dsDNA. RESULTS | |
| 0 4 Chp1 protein Chp1 is a subunit of the RNA-induced initiation of transcriptional gene silencing (RITS) complex. RESULTS | |
| 25 81 RNA-induced initiation of transcriptional gene silencing complex_assembly Chp1 is a subunit of the RNA-induced initiation of transcriptional gene silencing (RITS) complex. RESULTS | |
| 83 87 RITS complex_assembly Chp1 is a subunit of the RNA-induced initiation of transcriptional gene silencing (RITS) complex. RESULTS | |
| 15 19 Chp1 protein The partner of Chp1, Tas3, is bound between the barrel domain and the second domain of Chp1, and the linker between the two domains is also crucial for this interaction (Fig 3C). RESULTS | |
| 21 25 Tas3 protein The partner of Chp1, Tas3, is bound between the barrel domain and the second domain of Chp1, and the linker between the two domains is also crucial for this interaction (Fig 3C). RESULTS | |
| 48 61 barrel domain structure_element The partner of Chp1, Tas3, is bound between the barrel domain and the second domain of Chp1, and the linker between the two domains is also crucial for this interaction (Fig 3C). RESULTS | |
| 70 83 second domain structure_element The partner of Chp1, Tas3, is bound between the barrel domain and the second domain of Chp1, and the linker between the two domains is also crucial for this interaction (Fig 3C). RESULTS | |
| 87 91 Chp1 protein The partner of Chp1, Tas3, is bound between the barrel domain and the second domain of Chp1, and the linker between the two domains is also crucial for this interaction (Fig 3C). RESULTS | |
| 101 107 linker structure_element The partner of Chp1, Tas3, is bound between the barrel domain and the second domain of Chp1, and the linker between the two domains is also crucial for this interaction (Fig 3C). RESULTS | |
| 33 41 β-barrel structure_element It is probably unlikely that the β-barrel itself is sufficient to bind Tas3. RESULTS | |
| 71 75 Tas3 protein It is probably unlikely that the β-barrel itself is sufficient to bind Tas3. RESULTS | |
| 17 21 loop structure_element Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 25 29 Tas3 protein Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 39 45 strand structure_element Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 46 48 β3 structure_element Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 56 69 barrel domain structure_element Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 143 147 SMRT protein Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 148 155 peptide chemical Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 156 171 in complex with protein_state Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 172 177 SHARP protein Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 178 182 SPOC structure_element Interestingly, a loop in Tas3 contacts strand β3 of the barrel domain, at a location somewhat similar to that of the N-terminal segment of the SMRT peptide in complex with SHARP SPOC domain (Fig 3A). RESULTS | |
| 0 8 Mediator protein_type Mediator is a coactivator complex that promotes transcription by Pol II. RESULTS | |
| 65 71 Pol II complex_assembly Mediator is a coactivator complex that promotes transcription by Pol II. RESULTS | |
| 4 9 Med25 protein The Med25 subunit ACID is the target of the potent activator VP16 of the herpes simplex virus. RESULTS | |
| 18 22 ACID structure_element The Med25 subunit ACID is the target of the potent activator VP16 of the herpes simplex virus. RESULTS | |
| 61 65 VP16 protein The Med25 subunit ACID is the target of the potent activator VP16 of the herpes simplex virus. RESULTS | |
| 73 93 herpes simplex virus species The Med25 subunit ACID is the target of the potent activator VP16 of the herpes simplex virus. RESULTS | |
| 4 13 structure evidence The structure of ACID contains a helix at the C-terminus as well as an extended β1-β2 loop. RESULTS | |
| 17 21 ACID structure_element The structure of ACID contains a helix at the C-terminus as well as an extended β1-β2 loop. RESULTS | |
| 33 38 helix structure_element The structure of ACID contains a helix at the C-terminus as well as an extended β1-β2 loop. RESULTS | |
| 80 90 β1-β2 loop structure_element The structure of ACID contains a helix at the C-terminus as well as an extended β1-β2 loop. RESULTS | |
| 17 29 binding site site Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 34 38 VP16 protein Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 75 88 surface patch site Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 95 102 strands structure_element Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 103 105 β1 structure_element Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 110 112 β3 structure_element Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 134 139 SHARP protein Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 144 148 Tas3 protein Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 149 153 SPOC structure_element Nonetheless, the binding site for VP16 has been mapped to roughly the same surface patch, near strands β1 and β3, that is used by the SHARP and Tas3 SPOC domains for binding their partners. RESULTS | |
| 2 11 conserved protein_state A conserved surface patch in the FPA SPOC domain RESULTS | |
| 12 25 surface patch site A conserved surface patch in the FPA SPOC domain RESULTS | |
| 33 36 FPA protein A conserved surface patch in the FPA SPOC domain RESULTS | |
| 37 41 SPOC structure_element A conserved surface patch in the FPA SPOC domain RESULTS | |
| 19 23 SPOC structure_element An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 49 62 surface patch site An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 68 75 strands structure_element An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 76 78 β1 structure_element An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 80 82 β3 structure_element An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 84 86 β5 structure_element An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 91 93 β6 structure_element An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 102 111 conserved protein_state An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 118 123 plant taxonomy_domain An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 124 127 FPA protein An analysis of the SPOC domain indicates a large surface patch near strands β1, β3, β5 and β6 that is conserved among plant FPA homologs (Fig 4A). RESULTS | |
| 5 18 surface patch site This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 42 53 sub-patches site This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 69 75 Lys447 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 80 86 strand structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 87 89 β1 structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 92 98 Arg477 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 100 102 β3 structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 105 111 Tyr515 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 113 115 αB structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 121 127 Arg521 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 129 131 β5 structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 140 149 sub-patch site This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 164 170 His486 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 172 174 αA structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 177 183 Thr478 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 185 187 β3 structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 190 196 Val524 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 198 200 β5 structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 206 212 Phe534 residue_name_number This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 214 216 β6 structure_element This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 231 240 sub-patch site This surface patch can be broken into two sub-patches, with residues Lys447 (in strand β1), Arg477 (β3), Tyr515 (αB) and Arg521 (β5) in one sub-patch, and residues His486 (αA), Thr478 (β3), Val524 (β5) and Phe534 (β6) in the other sub-patch (Fig 4B). RESULTS | |
| 4 23 first surface patch site The first surface patch is electropositive in nature (Fig 4C), and residues Arg477 and Tyr515 are also conserved in the SHARP SPOC domain (Fig 1B). RESULTS | |
| 27 42 electropositive protein_state The first surface patch is electropositive in nature (Fig 4C), and residues Arg477 and Tyr515 are also conserved in the SHARP SPOC domain (Fig 1B). RESULTS | |
| 76 82 Arg477 residue_name_number The first surface patch is electropositive in nature (Fig 4C), and residues Arg477 and Tyr515 are also conserved in the SHARP SPOC domain (Fig 1B). RESULTS | |
| 87 93 Tyr515 residue_name_number The first surface patch is electropositive in nature (Fig 4C), and residues Arg477 and Tyr515 are also conserved in the SHARP SPOC domain (Fig 1B). RESULTS | |
| 103 112 conserved protein_state The first surface patch is electropositive in nature (Fig 4C), and residues Arg477 and Tyr515 are also conserved in the SHARP SPOC domain (Fig 1B). RESULTS | |
| 120 125 SHARP protein The first surface patch is electropositive in nature (Fig 4C), and residues Arg477 and Tyr515 are also conserved in the SHARP SPOC domain (Fig 1B). RESULTS | |
| 126 130 SPOC structure_element The first surface patch is electropositive in nature (Fig 4C), and residues Arg477 and Tyr515 are also conserved in the SHARP SPOC domain (Fig 1B). RESULTS | |
| 20 34 phosphorylated protein_state In fact, one of the phosphorylated residues of the SMRT peptide interacts with this surface patch (Fig 3A), suggesting that the FPA SPOC domain might also interact with a phosphorylated segment here. RESULTS | |
| 51 55 SMRT protein In fact, one of the phosphorylated residues of the SMRT peptide interacts with this surface patch (Fig 3A), suggesting that the FPA SPOC domain might also interact with a phosphorylated segment here. RESULTS | |
| 56 63 peptide chemical In fact, one of the phosphorylated residues of the SMRT peptide interacts with this surface patch (Fig 3A), suggesting that the FPA SPOC domain might also interact with a phosphorylated segment here. RESULTS | |
| 84 97 surface patch site In fact, one of the phosphorylated residues of the SMRT peptide interacts with this surface patch (Fig 3A), suggesting that the FPA SPOC domain might also interact with a phosphorylated segment here. RESULTS | |
| 128 131 FPA protein In fact, one of the phosphorylated residues of the SMRT peptide interacts with this surface patch (Fig 3A), suggesting that the FPA SPOC domain might also interact with a phosphorylated segment here. RESULTS | |
| 132 136 SPOC structure_element In fact, one of the phosphorylated residues of the SMRT peptide interacts with this surface patch (Fig 3A), suggesting that the FPA SPOC domain might also interact with a phosphorylated segment here. RESULTS | |
| 171 185 phosphorylated protein_state In fact, one of the phosphorylated residues of the SMRT peptide interacts with this surface patch (Fig 3A), suggesting that the FPA SPOC domain might also interact with a phosphorylated segment here. RESULTS | |
| 19 39 second surface patch site In comparison, the second surface patch is more hydrophobic in nature (Fig 4C). RESULTS | |
| 48 59 hydrophobic protein_state In comparison, the second surface patch is more hydrophobic in nature (Fig 4C). RESULTS | |
| 2 11 conserved protein_state A conserved surface patch of FPA SPOC domain. FIG | |
| 12 25 surface patch site A conserved surface patch of FPA SPOC domain. FIG | |
| 29 32 FPA protein A conserved surface patch of FPA SPOC domain. FIG | |
| 33 37 SPOC structure_element A conserved surface patch of FPA SPOC domain. FIG | |
| 38 41 FPA protein Two views of the molecular surface of FPA SPOC domain colored based on sequence conservation among plant FPA homologs. FIG | |
| 42 46 SPOC structure_element Two views of the molecular surface of FPA SPOC domain colored based on sequence conservation among plant FPA homologs. FIG | |
| 99 104 plant taxonomy_domain Two views of the molecular surface of FPA SPOC domain colored based on sequence conservation among plant FPA homologs. FIG | |
| 105 108 FPA protein Two views of the molecular surface of FPA SPOC domain colored based on sequence conservation among plant FPA homologs. FIG | |
| 16 25 conserved protein_state Residues in the conserved surface patch of FPA SPOC domain. FIG | |
| 26 39 surface patch site Residues in the conserved surface patch of FPA SPOC domain. FIG | |
| 43 46 FPA protein Residues in the conserved surface patch of FPA SPOC domain. FIG | |
| 47 51 SPOC structure_element Residues in the conserved surface patch of FPA SPOC domain. FIG | |
| 81 96 first sub-patch site The side chains of the residues are shown in stick models, colored orange in the first sub-patch and green in the second. (C). FIG | |
| 21 24 FPA protein Molecular surface of FPA SPOC domain colored based on electrostatic potential. FIG | |
| 25 29 SPOC structure_element Molecular surface of FPA SPOC domain colored based on electrostatic potential. FIG | |
| 62 65 FPA protein Testing the requirement of specific conserved amino acids for FPA functions RESULTS | |
| 45 54 conserved protein_state We next examined the potential impact of the conserved surface patch on FPA function in vivo. RESULTS | |
| 55 68 surface patch site We next examined the potential impact of the conserved surface patch on FPA function in vivo. RESULTS | |
| 72 75 FPA protein We next examined the potential impact of the conserved surface patch on FPA function in vivo. RESULTS | |
| 3 10 mutated experimental_method We mutated two residues, Arg477 and Tyr515, of the surface patch, which are also conserved in the SHARP SPOC domain (Fig 1B) and were found to be functionally important. RESULTS | |
| 25 31 Arg477 residue_name_number We mutated two residues, Arg477 and Tyr515, of the surface patch, which are also conserved in the SHARP SPOC domain (Fig 1B) and were found to be functionally important. RESULTS | |
| 36 42 Tyr515 residue_name_number We mutated two residues, Arg477 and Tyr515, of the surface patch, which are also conserved in the SHARP SPOC domain (Fig 1B) and were found to be functionally important. RESULTS | |
| 51 64 surface patch site We mutated two residues, Arg477 and Tyr515, of the surface patch, which are also conserved in the SHARP SPOC domain (Fig 1B) and were found to be functionally important. RESULTS | |
| 81 90 conserved protein_state We mutated two residues, Arg477 and Tyr515, of the surface patch, which are also conserved in the SHARP SPOC domain (Fig 1B) and were found to be functionally important. RESULTS | |
| 98 103 SHARP protein We mutated two residues, Arg477 and Tyr515, of the surface patch, which are also conserved in the SHARP SPOC domain (Fig 1B) and were found to be functionally important. RESULTS | |
| 104 108 SPOC structure_element We mutated two residues, Arg477 and Tyr515, of the surface patch, which are also conserved in the SHARP SPOC domain (Fig 1B) and were found to be functionally important. RESULTS | |
| 4 13 mutations experimental_method The mutations were introduced into a transgene designed to express FPA from its native control elements (promoter, introns and 3′ UTR). RESULTS | |
| 19 29 introduced experimental_method The mutations were introduced into a transgene designed to express FPA from its native control elements (promoter, introns and 3′ UTR). RESULTS | |
| 67 70 FPA protein The mutations were introduced into a transgene designed to express FPA from its native control elements (promoter, introns and 3′ UTR). RESULTS | |
| 35 53 stably transformed experimental_method The resulting transgenes were then stably transformed into an fpa-8 mutant background so that the impact of the mutations on FPA function could be assessed. RESULTS | |
| 62 67 fpa-8 gene The resulting transgenes were then stably transformed into an fpa-8 mutant background so that the impact of the mutations on FPA function could be assessed. RESULTS | |
| 68 74 mutant protein_state The resulting transgenes were then stably transformed into an fpa-8 mutant background so that the impact of the mutations on FPA function could be assessed. RESULTS | |
| 112 121 mutations experimental_method The resulting transgenes were then stably transformed into an fpa-8 mutant background so that the impact of the mutations on FPA function could be assessed. RESULTS | |
| 125 128 FPA protein The resulting transgenes were then stably transformed into an fpa-8 mutant background so that the impact of the mutations on FPA function could be assessed. RESULTS | |
| 35 56 expression constructs experimental_method Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 62 67 fpa-8 gene Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 88 97 wild-type protein_state Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 98 101 FPA protein Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 119 122 FPA protein Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 131 148 expression levels evidence Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 157 166 wild-type protein_state Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 222 225 FPA protein Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 241 244 RNA chemical Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 278 281 FPA protein Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 282 290 pre-mRNA chemical Control transformation of the same expression constructs into fpa-8 designed to express wild-type FPA protein restored FPA protein expression levels to near wild-type levels (panel A in S1 Fig) and rescued the function of FPA in controlling RNA 3′-end formation, for example in FPA pre-mRNA (panel B in S1 Fig). RESULTS | |
| 57 62 R477A mutant We examined independent transgenic lines expressing each R477A and Y515A mutation. RESULTS | |
| 67 72 Y515A mutant We examined independent transgenic lines expressing each R477A and Y515A mutation. RESULTS | |
| 73 81 mutation experimental_method We examined independent transgenic lines expressing each R477A and Y515A mutation. RESULTS | |
| 53 56 FPA protein In each case, we confirmed that detectable levels of FPA protein expression were restored close to wild-type levels in protein blot analyses using antibodies that specifically recognize FPA (S2 Fig). RESULTS | |
| 99 108 wild-type protein_state In each case, we confirmed that detectable levels of FPA protein expression were restored close to wild-type levels in protein blot analyses using antibodies that specifically recognize FPA (S2 Fig). RESULTS | |
| 119 131 protein blot experimental_method In each case, we confirmed that detectable levels of FPA protein expression were restored close to wild-type levels in protein blot analyses using antibodies that specifically recognize FPA (S2 Fig). RESULTS | |
| 186 189 FPA protein In each case, we confirmed that detectable levels of FPA protein expression were restored close to wild-type levels in protein blot analyses using antibodies that specifically recognize FPA (S2 Fig). RESULTS | |
| 35 48 surface patch site We then examined the impact of the surface patch mutations on FPA’s function in controlling RNA 3′-end formation by determining whether the mutant proteins functioned in FPA autoregulation and the repression of FLC expression. RESULTS | |
| 49 58 mutations experimental_method We then examined the impact of the surface patch mutations on FPA’s function in controlling RNA 3′-end formation by determining whether the mutant proteins functioned in FPA autoregulation and the repression of FLC expression. RESULTS | |
| 62 65 FPA protein We then examined the impact of the surface patch mutations on FPA’s function in controlling RNA 3′-end formation by determining whether the mutant proteins functioned in FPA autoregulation and the repression of FLC expression. RESULTS | |
| 140 146 mutant protein_state We then examined the impact of the surface patch mutations on FPA’s function in controlling RNA 3′-end formation by determining whether the mutant proteins functioned in FPA autoregulation and the repression of FLC expression. RESULTS | |
| 170 173 FPA protein We then examined the impact of the surface patch mutations on FPA’s function in controlling RNA 3′-end formation by determining whether the mutant proteins functioned in FPA autoregulation and the repression of FLC expression. RESULTS | |
| 211 214 FLC gene We then examined the impact of the surface patch mutations on FPA’s function in controlling RNA 3′-end formation by determining whether the mutant proteins functioned in FPA autoregulation and the repression of FLC expression. RESULTS | |
| 0 3 FPA protein FPA autoregulates its expression by promoting cleavage and polyadenylation within intron 1 of its own pre-mRNA, resulting in a truncated transcript that does not encode functional protein. RESULTS | |
| 102 110 pre-mRNA chemical FPA autoregulates its expression by promoting cleavage and polyadenylation within intron 1 of its own pre-mRNA, resulting in a truncated transcript that does not encode functional protein. RESULTS | |
| 8 29 RNA gel blot analyses experimental_method We used RNA gel blot analyses to reveal that in each of three independent transgenic lines for each single mutant, rescue of proximally polyadenylated FPA pre-mRNA can be detected (Fig 5A and 5B). RESULTS | |
| 107 113 mutant protein_state We used RNA gel blot analyses to reveal that in each of three independent transgenic lines for each single mutant, rescue of proximally polyadenylated FPA pre-mRNA can be detected (Fig 5A and 5B). RESULTS | |
| 151 154 FPA protein We used RNA gel blot analyses to reveal that in each of three independent transgenic lines for each single mutant, rescue of proximally polyadenylated FPA pre-mRNA can be detected (Fig 5A and 5B). RESULTS | |
| 155 163 pre-mRNA chemical We used RNA gel blot analyses to reveal that in each of three independent transgenic lines for each single mutant, rescue of proximally polyadenylated FPA pre-mRNA can be detected (Fig 5A and 5B). RESULTS | |
| 79 82 FPA protein We therefore conclude that neither of these mutations disrupted the ability of FPA to promote RNA 3′-end formation in its own transcript. RESULTS | |
| 21 24 FPA protein Impact of individual FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA. FIG | |
| 25 29 SPOC structure_element Impact of individual FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA. FIG | |
| 37 46 mutations experimental_method Impact of individual FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA. FIG | |
| 81 84 FPA protein Impact of individual FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA. FIG | |
| 85 93 pre-mRNA chemical Impact of individual FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA. FIG | |
| 0 12 RNA gel blot experimental_method RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 25 27 WT protein_state RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 28 39 A. thaliana species RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 67 73 plants taxonomy_domain RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 74 79 fpa-8 gene RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 84 89 fpa-8 gene RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 90 97 mutants protein_state RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 116 119 FPA protein RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 121 130 FPA R477A mutant RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 139 142 FPA protein RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 144 153 FPA Y515A mutant RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 182 187 mRNAs chemical RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing either FPA::FPA R477A (A), or FPA::FPA Y515A (B) using poly(A)+ purified mRNAs. FIG | |
| 45 48 FPA protein A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 49 53 mRNA chemical A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 73 76 FPA protein A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 86 91 mRNAs chemical A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 45 48 FPA protein A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 49 53 mRNA chemical A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 73 76 FPA protein A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 86 91 mRNAs chemical A probe corresponding to the 5’UTR region of FPA mRNA was used to detect FPA specific mRNAs. FIG | |
| 39 42 FPA protein Proximally and distally polyadenylated FPA transcripts are marked with arrows. FIG | |
| 103 106 FPA protein The ratio of distal:proximal polyadenylated forms is given under each lane. (C,D) Impact of individual FPA SPOC domain mutations on FLC transcript levels. FIG | |
| 107 111 SPOC structure_element The ratio of distal:proximal polyadenylated forms is given under each lane. (C,D) Impact of individual FPA SPOC domain mutations on FLC transcript levels. FIG | |
| 119 128 mutations experimental_method The ratio of distal:proximal polyadenylated forms is given under each lane. (C,D) Impact of individual FPA SPOC domain mutations on FLC transcript levels. FIG | |
| 132 135 FLC gene The ratio of distal:proximal polyadenylated forms is given under each lane. (C,D) Impact of individual FPA SPOC domain mutations on FLC transcript levels. FIG | |
| 0 7 qRT-PCR experimental_method qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 42 45 RNA chemical qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 67 72 fpa-8 gene qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 79 82 FPA protein qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 83 86 YFP experimental_method qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 91 94 FPA protein qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 96 105 FPA R477A mutant qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 111 114 FPA protein qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 116 125 FPA Y515A mutant qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 130 136 plants taxonomy_domain qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, 35S::FPA:YFP and FPA::FPA R477A (C), FPA::FPA Y515A (D) plants. FIG | |
| 0 10 Histograms evidence Histograms show mean values ±SE for three independent PCR amplifications of three biological replicates. FIG | |
| 54 57 PCR experimental_method Histograms show mean values ±SE for three independent PCR amplifications of three biological replicates. FIG | |
| 0 10 Histograms evidence Histograms show mean values ±SE for three independent PCR amplifications of three biological replicates. FIG | |
| 54 57 PCR experimental_method Histograms show mean values ±SE for three independent PCR amplifications of three biological replicates. FIG | |
| 78 81 FPA protein We next examined whether the corresponding mutations disrupted the ability of FPA to control FLC expression. RESULTS | |
| 93 96 FLC gene We next examined whether the corresponding mutations disrupted the ability of FPA to control FLC expression. RESULTS | |
| 8 15 RT-qPCR experimental_method We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 45 48 FLC gene We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 49 53 mRNA chemical We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 119 126 mutated protein_state We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 127 130 FPA protein We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 163 166 FLC gene We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 179 184 fpa-8 gene We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 185 192 mutants protein_state We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 215 224 wild-type protein_state We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 253 256 FPA protein We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 257 261 SPOC structure_element We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 262 271 conserved protein_state We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 272 277 patch site We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 278 284 mutant protein_state We used RT-qPCR to measure the expression of FLC mRNA and found that in each independent transgenic line encoding each mutated FPA protein, the elevated levels of FLC detected in fpa-8 mutants were restored to near wild-type levels by expression of the FPA SPOC conserved patch mutant proteins (Fig 5C and 5D). RESULTS | |
| 11 24 surface patch site Since each surface patch mutation appeared to be insufficient to disrupt FPA functions on its own, we combined both mutations into the same transgene. RESULTS | |
| 25 33 mutation experimental_method Since each surface patch mutation appeared to be insufficient to disrupt FPA functions on its own, we combined both mutations into the same transgene. RESULTS | |
| 73 76 FPA protein Since each surface patch mutation appeared to be insufficient to disrupt FPA functions on its own, we combined both mutations into the same transgene. RESULTS | |
| 33 42 wild-type protein_state We could again confirm that near wild-type levels of FPA protein were expressed from three independent transgenic lines expressing the FPA R477A;Y515A doubly mutated protein in an fpa-8 mutant background (S3 Fig). RESULTS | |
| 53 56 FPA protein We could again confirm that near wild-type levels of FPA protein were expressed from three independent transgenic lines expressing the FPA R477A;Y515A doubly mutated protein in an fpa-8 mutant background (S3 Fig). RESULTS | |
| 135 150 FPA R477A;Y515A mutant We could again confirm that near wild-type levels of FPA protein were expressed from three independent transgenic lines expressing the FPA R477A;Y515A doubly mutated protein in an fpa-8 mutant background (S3 Fig). RESULTS | |
| 151 165 doubly mutated protein_state We could again confirm that near wild-type levels of FPA protein were expressed from three independent transgenic lines expressing the FPA R477A;Y515A doubly mutated protein in an fpa-8 mutant background (S3 Fig). RESULTS | |
| 180 185 fpa-8 gene We could again confirm that near wild-type levels of FPA protein were expressed from three independent transgenic lines expressing the FPA R477A;Y515A doubly mutated protein in an fpa-8 mutant background (S3 Fig). RESULTS | |
| 186 192 mutant protein_state We could again confirm that near wild-type levels of FPA protein were expressed from three independent transgenic lines expressing the FPA R477A;Y515A doubly mutated protein in an fpa-8 mutant background (S3 Fig). RESULTS | |
| 14 29 FPA R477A;Y515A mutant We found that FPA R477A;Y515A protein functioned like wild-type FPA to restore FPA pre-mRNA proximal polyadenylation (Fig 6A) and FLC expression to wild-type levels (Fig 6B). RESULTS | |
| 54 63 wild-type protein_state We found that FPA R477A;Y515A protein functioned like wild-type FPA to restore FPA pre-mRNA proximal polyadenylation (Fig 6A) and FLC expression to wild-type levels (Fig 6B). RESULTS | |
| 64 67 FPA protein We found that FPA R477A;Y515A protein functioned like wild-type FPA to restore FPA pre-mRNA proximal polyadenylation (Fig 6A) and FLC expression to wild-type levels (Fig 6B). RESULTS | |
| 79 82 FPA protein We found that FPA R477A;Y515A protein functioned like wild-type FPA to restore FPA pre-mRNA proximal polyadenylation (Fig 6A) and FLC expression to wild-type levels (Fig 6B). RESULTS | |
| 83 91 pre-mRNA chemical We found that FPA R477A;Y515A protein functioned like wild-type FPA to restore FPA pre-mRNA proximal polyadenylation (Fig 6A) and FLC expression to wild-type levels (Fig 6B). RESULTS | |
| 130 133 FLC gene We found that FPA R477A;Y515A protein functioned like wild-type FPA to restore FPA pre-mRNA proximal polyadenylation (Fig 6A) and FLC expression to wild-type levels (Fig 6B). RESULTS | |
| 148 157 wild-type protein_state We found that FPA R477A;Y515A protein functioned like wild-type FPA to restore FPA pre-mRNA proximal polyadenylation (Fig 6A) and FLC expression to wild-type levels (Fig 6B). RESULTS | |
| 17 20 FPA protein Impact of double FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA and FLC expression. FIG | |
| 21 25 SPOC structure_element Impact of double FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA and FLC expression. FIG | |
| 33 42 mutations experimental_method Impact of double FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA and FLC expression. FIG | |
| 77 80 FPA protein Impact of double FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA and FLC expression. FIG | |
| 81 89 pre-mRNA chemical Impact of double FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA and FLC expression. FIG | |
| 94 97 FLC gene Impact of double FPA SPOC domain mutations on alternative polyadenylation of FPA pre-mRNA and FLC expression. FIG | |
| 4 16 RNA gel blot experimental_method (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 29 31 WT protein_state (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 32 43 A. thaliana species (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 71 77 plants taxonomy_domain (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 78 83 fpa-8 gene (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 88 93 fpa-8 gene (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 94 101 mutants protein_state (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 113 116 FPA protein (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 118 133 FPA R477A;Y515A mutant (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 158 163 mRNAs chemical (A) RNA gel blot analysis of WT A. thaliana accession Columbia (Col-0) plants fpa-8 and fpa-8 mutants expressing FPA::FPA R477A;Y515A using poly(A)+ purified mRNAs. FIG | |
| 65 68 FPA protein Black arrows indicate the proximally and distally polyadenylated FPA mRNAs. FIG | |
| 69 74 mRNAs chemical Black arrows indicate the proximally and distally polyadenylated FPA mRNAs. FIG | |
| 0 7 qRT-PCR experimental_method qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, and FPA::FPA R477A;Y515A plants. FIG | |
| 42 45 RNA chemical qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, and FPA::FPA R477A;Y515A plants. FIG | |
| 67 72 fpa-8 gene qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, and FPA::FPA R477A;Y515A plants. FIG | |
| 78 81 FPA protein qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, and FPA::FPA R477A;Y515A plants. FIG | |
| 83 98 FPA R477A;Y515A mutant qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, and FPA::FPA R477A;Y515A plants. FIG | |
| 99 105 plants taxonomy_domain qRT-PCR analysis was performed with total RNA purified from Col-0, fpa-8, and FPA::FPA R477A;Y515A plants. FIG | |
| 46 50 SPOC structure_element Together our findings suggest that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation, or that this combination of mutations is not sufficient to critically disrupt the function of the FPA SPOC domain. RESULTS | |
| 90 93 FPA protein Together our findings suggest that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation, or that this combination of mutations is not sufficient to critically disrupt the function of the FPA SPOC domain. RESULTS | |
| 108 111 RNA chemical Together our findings suggest that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation, or that this combination of mutations is not sufficient to critically disrupt the function of the FPA SPOC domain. RESULTS | |
| 158 167 mutations experimental_method Together our findings suggest that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation, or that this combination of mutations is not sufficient to critically disrupt the function of the FPA SPOC domain. RESULTS | |
| 228 231 FPA protein Together our findings suggest that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation, or that this combination of mutations is not sufficient to critically disrupt the function of the FPA SPOC domain. RESULTS | |
| 232 236 SPOC structure_element Together our findings suggest that either the SPOC domain is not required for the role of FPA in regulating RNA 3′-end formation, or that this combination of mutations is not sufficient to critically disrupt the function of the FPA SPOC domain. RESULTS | |
| 24 33 mutations experimental_method Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 41 46 SHARP protein Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 47 51 SPOC structure_element Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 89 105 unphosphorylated protein_state Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 106 110 SMRT protein Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 111 119 peptides chemical Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 202 205 FPA protein Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 206 210 SPOC structure_element Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |
| 273 277 SPOC structure_element Since the corresponding mutations in the SHARP SPOC domain do disrupt its recognition of unphosphorylated SMRT peptides, these observations may reinforce the idea that the features and functions of the FPA SPOC domain differ from those of the only other well-characterized SPOC domain. RESULTS | |