+Open data
-Basic information
Entry | Database: PDB / ID: 3k7a | ||||||
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Title | Crystal Structure of an RNA polymerase II-TFIIB complex | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA polymerase II / TFIIB / DNA-binding / DNA-directed RNA polymerase / Isopeptide bond / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Zinc-finger / DNA damage / DNA repair / Transcription regulation | ||||||
Function / homology | Function and homology information RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / positive regulation of transcription regulatory region DNA binding / transcription preinitiation complex / 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 ...RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / positive regulation of transcription regulatory region DNA binding / transcription preinitiation complex / 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 polymerase II general transcription initiation factor activity / 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 II complex binding / 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 / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / 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 / molecular replacement / Resolution: 3.8 Å | ||||||
Authors | Liu, X. / Bushnell, D.A. / Wang, D. / Calero, G. / Kornberg, R.D. | ||||||
Citation | Journal: Science / Year: 2010 Title: Structure of an RNA polymerase II-TFIIB complex and the transcription initiation mechanism. Authors: Liu, X. / Bushnell, D.A. / Wang, D. / Calero, G. / 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 | 3k7a.cif.gz | 767.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k7a.ent.gz | 603.3 KB | Display | PDB format |
PDBx/mmJSON format | 3k7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/3k7a ftp://data.pdbj.org/pub/pdb/validation_reports/k7/3k7a | HTTPS FTP |
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-Related structure data
Related structure data | 1r5uS S: Starting model for refinement |
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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-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C / Production host: 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 genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB150, RPB2, RPO22, YOR151C / Production host: 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 genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB3, YIL021W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370 |
#7: Protein | Mass: 14308.161 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB9, YGL070C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P27999 |
#9: Protein | Mass: 13633.493 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB11, YOL005C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38902 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#4: Protein | Mass: 25117.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA7, RPB5, RPC9, YBR1204, YBR154C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434 |
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#5: Protein | Mass: 17931.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: P9677.8, RPB6, RPO26, YPR187W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435 |
#6: Protein | Mass: 16525.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436 |
#8: Protein | Mass: 8290.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139 |
#10: Protein | Mass: 7729.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Protein A tag on RPB1 CTD Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB12, RPC10, YHR143BW, YHR143W-A / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422 |
-Protein / Non-polymers , 2 types, 10 molecules M
#11: Protein | Mass: 38257.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: P9513.4, SUA7, YPR086W / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P29055 |
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#12: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.57 Å3/Da / Density % sol: 73.1 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 1.2 M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 8, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.8→210.49 Å / Num. obs: 89990 / % possible obs: 98.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 9.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R5U WITHOUT CHAIN M Resolution: 3.8→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.874 / Occupancy max: 1 / Occupancy min: 1 / SU B: 110.637 / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.728 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK / Bsol: 136.857 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 500 Å2 / Biso mean: 188.144 Å2 / Biso min: 36.88 Å2
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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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