+Open data
-Basic information
Entry | Database: PDB / ID: 1wcm | ||||||
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Title | Complete 12-Subunit RNA Polymerase II at 3.8 Angstrom | ||||||
Components |
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Keywords | TRANSCRIPTION / DNA-BINDING / DNA-DIRECTED RNA POLYMERASE / DNA-DEPENDENT RNA POLYMERASE / CELLULAR RNA POLYMERASE / MULTISUBUNIT CO / METAL- BINDING / NUCLEAR PROTEIN / PHOSPHORYLATION / TRANSFERASE / ZINC / ZINC-FINGER | ||||||
Function / homology | Function and homology information RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / 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 / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wcm.cif.gz | 789.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wcm.ent.gz | 651.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/1wcm ftp://data.pdbj.org/pub/pdb/validation_reports/wc/1wcm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA-DIRECTED RNA POLYMERASE II ... , 7 types, 7 molecules ABCDGIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16370, DNA-directed RNA polymerase |
#4: Protein | Mass: 20333.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: NUMBERING OF RESIUDES D10-D24 IS ARBITRARY Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: DNA-directed RNA polymerase |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: DNA-directed RNA polymerase |
#9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P27999, DNA-directed RNA polymerase |
#11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38902, DNA-directed RNA polymerase |
-DNA-DIRECTED RNA POLYMERASES I, II, AND III ... , 4 types, 4 molecules EFHL
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20434, DNA-directed RNA polymerase |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20435, DNA-directed RNA polymerase |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20436, DNA-directed RNA polymerase |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40422, DNA-directed RNA polymerase |
-Protein , 1 types, 1 molecules J
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22139, DNA-directed RNA polymerase |
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-Non-polymers , 2 types, 9 molecules
#13: Chemical | ChemComp-ZN / #14: Chemical | ChemComp-MG / | |
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-Details
Compound details | FUNCTION: DNA-DEPENDENT RNA POLYMERASE CATALYZES THE TRANSCRIPTION OF DNA INTO RNA USING THE FOUR ...FUNCTION: DNA-DEPENDENT RNA POLYMERASE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 6.14 Å3/Da / Density % sol: 80 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97924 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 121866 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 3.8→3.95 Å / % possible all: 97 |
-Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 15.4597 Å2 / ksol: 0.219914 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.8→50 Å
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Refine LS restraints |
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Xplor file |
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