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Open data
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Basic information
| Entry | Database: PDB / ID: 2nvt | ||||||
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| Title | RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSFERASE/DNA-RNA HYBRID / MRNA / MULTIPROTEIN COMPLEX / MOLECULAR MACHINE / DNA / TRANSFERASE-DNA-RNA HYBRID COMPLEX | ||||||
| Function / homology | Function and homology informationRNA 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 / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...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 / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / 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 / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.36 Å | ||||||
Authors | Wang, D. / Bushnell, D.A. / Westover, K.D. / Kaplan, C.D. / Kornberg, R.D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006Title: Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis Authors: Wang, D. / Bushnell, D.A. / Westover, K.D. / Kaplan, C.D. / Kornberg, R.D. | ||||||
| History |
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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 | 2nvt.cif.gz | 754.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2nvt.ent.gz | 589.6 KB | Display | PDB format |
| PDBx/mmJSON format | 2nvt.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2nvt_validation.pdf.gz | 894.8 KB | Display | wwPDB validaton report |
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| Full document | 2nvt_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML | 2nvt_validation.xml.gz | 144.5 KB | Display | |
| Data in CIF | 2nvt_validation.cif.gz | 198.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/2nvt ftp://data.pdbj.org/pub/pdb/validation_reports/nv/2nvt | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2e2hC ![]() 2e2iC ![]() 2e2jC ![]() 2nvqC ![]() 2nvxC ![]() 2nvyC ![]() 2nvzC ![]() 2yu9C ![]() 1sfoS S: Starting model for refinement C: citing same article ( |
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| Similar 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 chain , 2 types, 2 molecules TN
| #2: DNA chain | Mass: 6389.133 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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| #3: DNA chain | Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-DNA-directed RNA polymerase II ... , 5 types, 5 molecules ABCIK
| #4: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #5: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #6: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #10: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #12: 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
| #7: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #8: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #9: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
| #13: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-RNA chain / Protein , 2 types, 2 molecules RJ
| #11: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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| #1: RNA chain | Mass: 3223.028 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 11 molecules 




| #14: Chemical | ChemComp-G2P / | ||
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| #15: Chemical | ChemComp-ZN / #16: Chemical | |
-Details
| Has protein modification | Y |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.25 % | ||||||||||||||||||||||||||||||||||||
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| Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 200mM NH4OAc, 150mM Mg(OAc)2, 50mM Hepes, pH 7.0, 5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
| Components of the solutions |
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-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
| Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2006 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
| Reflection | Resolution: 3.36→40 Å / Num. obs: 95301 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rsym value: 0.125 / Net I/σ(I): 8 |
| Reflection shell | Resolution: 3.36→3.5 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.541 / % possible all: 94.8 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 1SFO Resolution: 3.36→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 70.123 / SU ML: 0.5 / Cross valid method: THROUGHOUT / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 124.679 Å2
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| Refinement step | Cycle: LAST / Resolution: 3.36→40 Å
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| Refine LS restraints |
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| LS refinement shell | Resolution: 3.36→3.448 Å / Total num. of bins used: 20
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