+Open data
-Basic information
Entry | Database: PDB / ID: 1y14 | ||||||
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Title | Crystal structure of yeast subcomplex of Rpb4 and Rpb7 | ||||||
Components |
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Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / Dual incision in TC-NER / positive regulation of translational initiation / RNA polymerase II, core complex / translation initiation factor binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / mRNA processing / single-stranded DNA binding / transcription by RNA polymerase II / single-stranded RNA binding / nucleotide binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 2.3 Å | ||||||
Authors | Armache, K.-J. / Mitterweger, S. / Meinhart, A. / Cramer, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Structures of Complete RNA Polymerase II and Its Subcomplex, Rpb4/7 Authors: Armache, K.-J. / Mitterweger, S. / Meinhart, A. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y14.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y14.ent.gz | 100.7 KB | Display | PDB format |
PDBx/mmJSON format | 1y14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y14 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y14 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 21436.705 Da / Num. of mol.: 2 / Fragment: residues 35-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P20433, DNA-directed RNA polymerase #2: Protein | Mass: 19081.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: P34087, DNA-directed RNA polymerase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.37 % |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Refinement | Method to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.228 / σ(F): 2 | ||||||||||||
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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