+Open data
-Basic information
Entry | Database: PDB / ID: 3k1f | ||||||
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Title | Crystal structure of RNA Polymerase II in complex with TFIIB | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA Polymerase II / TFIIB / Transcription Factor / Transcription Initiation / DNA-binding / DNA-directed RNA polymerase / Isopeptide bond / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Zinc-finger / DNA damage / DNA repair / mRNA processing / Initiation factor | ||||||
Function / homology | Function and homology information transcription preinitiation complex assembly / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation ...transcription preinitiation complex assembly / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / positive regulation of translational initiation / 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 / translation initiation factor binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / translation initiation factor activity / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / nucleotide binding / 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: 4.3 Å | ||||||
Authors | Kostrewa, D. / Zeller, M.E. / Armache, K.-J. / Seizl, M. / Leike, K. / Thomm, M. / Cramer, P. | ||||||
Citation | Journal: Nature / Year: 2009 Title: RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Authors: Kostrewa, D. / Zeller, M.E. / Armache, K.J. / Seizl, M. / Leike, K. / Thomm, M. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k1f.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3k1f.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 3k1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/3k1f ftp://data.pdbj.org/pub/pdb/validation_reports/k1/3k1f | HTTPS FTP |
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-Related structure data
Related structure data | 3houS 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 ... , 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: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34087, 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 subunit ... , 5 types, 5 molecules EFHJL
#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 |
#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 |
#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 / Non-polymers , 2 types, 10 molecules M
#13: Protein | Mass: 18691.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: B3LK56, UniProt: P29055*PLUS |
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#14: Chemical | ChemComp-ZN / |
-Details
Sequence details | THE B-LINKER AND B-CYCLIN DOMAIN OF TFIIB (CHAIN M, RESIDUES 84-214) WERE FITTED AS POLY-ALANINE ...THE B-LINKER AND B-CYCLIN DOMAIN OF TFIIB (CHAIN M, RESIDUES 84-214) WERE FITTED AS POLY-ALANINE USING UNK RESIDUE NAMES DUE TO EXPERIMENT |
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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: 5.82 Å3/Da / Density % sol: 78.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 800 mM sodium ammonium tartrate, 100 mM HEPES pH 7.5, 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Details: silicon crystal monochromator |
Radiation | Monochromator: Silicon crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 4.3→40 Å / Num. all: 83919 / Num. obs: 83919 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.13 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 4.3→4.3 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 6050 / Rsym value: 0.99 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: First 12-subunit RNA Polymerase II from PDB entry 3HOU Resolution: 4.3→39.69 Å Isotropic thermal model: Overall anisotropic temperature factor, one TLS group for all atoms, one group isotropic temperature factor for each residue Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: REFINEMENT WAS DONE AGAINST THE STRUCTURE FACTORS WITH FRIEDEL PAIRS MERGED AND A SHARPENING B-FACTOR OF -80 A**2 APPLIED. THE STRUCTURE WAS REFINED WITH ONE TLS GROUP FOR ALL ATOMS AND ...Details: REFINEMENT WAS DONE AGAINST THE STRUCTURE FACTORS WITH FRIEDEL PAIRS MERGED AND A SHARPENING B-FACTOR OF -80 A**2 APPLIED. THE STRUCTURE WAS REFINED WITH ONE TLS GROUP FOR ALL ATOMS AND ISOTROPIC GROUP B-FACTORS FOR WHOLE RESIDUES. ADDITIONAL DISTANCE RESTRAINTS WERE APPLIED TO STABILIZE THE ZINC COORDINATION SPHERE AND SECONDARY STRUCTURAL ELEMENTS. THE BUSTER ELECTRON DENSITY MAP COEFFICIENTS ARE AVAILABLE UPON REQUEST FROM DIRK KOSTREWA.
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Displacement parameters | Biso mean: 124.4 Å2
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Refine analyze | Luzzati coordinate error obs: 1.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.3→39.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.3→4.41 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 97.8862 Å / Origin y: 54.753 Å / Origin z: -2.3668 Å
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Refinement TLS group |
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