+Open data
-Basic information
Entry | Database: PDB / ID: 2nvq | ||||||
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Title | RNA Polymerase II Elongation Complex in 150 mM Mg+2 with 2'dUTP | ||||||
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 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 / cytoplasmic stress granule / peroxisome / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Wang, D. / Bushnell, D.A. / Westover, K.D. / Kaplan, C.D. / Kornberg, R.D. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nvq.cif.gz | 762 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nvq.ent.gz | 596.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/2nvq ftp://data.pdbj.org/pub/pdb/validation_reports/nv/2nvq | HTTPS FTP |
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-Related structure data
Related structure data | 2e2hC 2e2iC 2e2jC 2nvtC 2nvxC 2nvyC 2nvzC 2yu9C 1sfoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 8534.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4286.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P04050, DNA-directed RNA polymerase |
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#5: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P08518, DNA-directed RNA polymerase |
#6: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P16370, DNA-directed RNA polymerase |
#10: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P27999, DNA-directed RNA polymerase |
#12: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P38902, DNA-directed RNA polymerase |
-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) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P20434, DNA-directed RNA polymerase |
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#8: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P20435, DNA-directed RNA polymerase |
#9: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P20436, DNA-directed RNA polymerase |
#13: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P40422, DNA-directed RNA polymerase |
-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) Saccharomyces cerevisiae (brewer's yeast) / Strain: CB010 Delta RPB4 / References: UniProt: P22139, DNA-directed RNA polymerase |
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#1: RNA chain | Mass: 3264.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 11 molecules
#14: Chemical | ChemComp-DUT / | ||
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#15: Chemical | ChemComp-ZN / #16: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.12 % | ||||||||||||||||||||||||||||||||||||
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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 source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.45 Å / Num. obs: 146322 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.142 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.746 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SFO Resolution: 2.9→48.45 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.878 / SU B: 44.402 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.758 / ESU R Free: 0.387 / 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: 59.84 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→48.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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