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Open data
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Basic information
Entry | Database: PDB / ID: 3k1f | ||||||
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Title | Crystal structure of RNA Polymerase II in complex with TFIIB | ||||||
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![]() | 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 | ![]() 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 / RNA polymerase II core complex assembly / 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 / RNA polymerase II core complex assembly / positive regulation of transcription regulatory region DNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / RNA polymerase II transcribes snRNA genes / 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 II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / acetyltransferase activity / Dual incision in TC-NER / RNA polymerase II general transcription initiation factor activity / transcription elongation by RNA polymerase I / RNA polymerase II core promoter sequence-specific DNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / translation initiation factor activity / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kostrewa, D. / Zeller, M.E. / Armache, K.-J. / Seizl, M. / Leike, K. / Thomm, M. / Cramer, P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 515.6 KB | Display | ![]() |
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Full document | ![]() | 591.4 KB | Display | |
Data in XML | ![]() | 77.8 KB | Display | |
Data in CIF | ![]() | 119.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3houS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() ![]() |
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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: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#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 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) ![]() ![]() |
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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) ![]() ![]() |
#10: Protein | Mass: 8290.732 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 / Non-polymers , 2 types, 10 molecules M![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#13: Protein | Mass: 18691.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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