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Open data
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Basic information
| Entry | Database: PDB / ID: 1wcm | ||||||
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| Title | Complete 12-Subunit RNA Polymerase II at 3.8 Angstrom | ||||||
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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 informationRNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / 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 / Formation of TC-NER Pre-Incision Complex / Estrogen-dependent gene expression / 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 1 Promoter / 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 / Formation of TC-NER Pre-Incision Complex / Estrogen-dependent gene expression / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / 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 Polymerase II Pre-transcription Events / RNA-templated transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / termination of RNA polymerase II transcription / Dual incision in TC-NER / termination of RNA polymerase I transcription / transcription by RNA polymerase III / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / translesion synthesis / DNA-templated transcription elongation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / transcription by RNA polymerase II / ribonucleoside binding / cytoplasmic stress granule / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / nucleoplasm / zinc ion binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| 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: 2005Title: 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. |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 1wcm.cif.gz | 793.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb1wcm.ent.gz | 631.6 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
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Links
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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) ![]() |
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| #2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #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.) ![]() Production host: ![]() |
| #7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
| #9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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| #6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-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) ![]() |
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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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| Has protein modification | Y |
-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 |
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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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