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Yorodumi- PDB-5m9d: Solution structure of Rtt103 CTD-interacting domain bound to a Se... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m9d | |||||||||
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Title | Solution structure of Rtt103 CTD-interacting domain bound to a Ser2Ser7 phosphorylated CTD peptide | |||||||||
Components |
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Keywords | TRANSCRIPTION / RNAPII C-terminal domain / CTD-interacting domain / phosphorylation | |||||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain phosphoserine binding / retrotransposon silencing / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes ...RNA polymerase II C-terminal domain phosphoserine binding / retrotransposon silencing / mRNA 3'-end processing / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase II complex binding / Gap-filling DNA repair synthesis and ligation in TC-NER / translesion synthesis / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / site of double-strand break / transcription by RNA polymerase II / chromatin / mitochondrion / DNA binding / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Jasnovidova, O. / Kubicek, K. / Stefl, R. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structure and dynamics of the RNAPII CTDsome with Rtt103. Authors: Jasnovidova, O. / Klumpler, T. / Kubicek, K. / Kalynych, S. / Plevka, P. / Stefl, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m9d.cif.gz | 975.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m9d.ent.gz | 822.6 KB | Display | PDB format |
PDBx/mmJSON format | 5m9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/5m9d ftp://data.pdbj.org/pub/pdb/validation_reports/m9/5m9d | HTTPS FTP |
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-Related structure data
Related structure data | 5m48C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 16569.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: RTT103, YDR289C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05543 |
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#2: Protein/peptide | Mass: 1965.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: P / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1 mM [U-13C; U-15N] CTD-interacting domain of Rtt103p, 1.5 mM THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER-PRO-SEP-TYR-SEP-PRO-THR-SER, 90% H2O/10% D2O Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Details: 35mM KH2PO4 100mM KCl / Ionic strength: 100 mM / Label: 1 / pH: 6.8 / Pressure: 760 mmHg / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 6 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |