+Open data
-Basic information
Entry | Database: PDB / ID: 1r5u | ||||||
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Title | RNA POLYMERASE II TFIIB COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION / Zinc Ribbon | ||||||
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 / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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 Pre-transcription Events / RNA-templated transcription / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||
Authors | Bushnell, D.A. / Westover, K.D. / Davis, R. / Kornberg, R.D. | ||||||
Citation | Journal: Science / Year: 2004 Title: Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Authors: Bushnell, D.A. / Westover, K.D. / Davis, R.E. / Kornberg, R.D. | ||||||
History |
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Remark 999 | SEQUENCE The residues of chain M are marked as unknown due to lack of electron density. The ...SEQUENCE The residues of chain M are marked as unknown due to lack of electron density. The sequence of the chain M corresponds to transcription initiation factor IIB, SWS entry P29055. The allignment within the chain is unclear. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r5u.cif.gz | 673.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r5u.ent.gz | 539.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r5u_validation.pdf.gz | 564.7 KB | Display | wwPDB validaton report |
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Full document | 1r5u_full_validation.pdf.gz | 818.8 KB | Display | |
Data in XML | 1r5u_validation.xml.gz | 155.4 KB | Display | |
Data in CIF | 1r5u_validation.cif.gz | 206.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/1r5u ftp://data.pdbj.org/pub/pdb/validation_reports/r5/1r5u | HTTPS FTP |
-Related structure data
Related structure data | 1i6hS 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 ... , 5 types, 5 molecules ABCIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / 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) / Strain: DELTA-RPB4 / 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) / Strain: DELTA-RPB4 / References: UniProt: P16370, DNA-directed RNA polymerase |
#7: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P27999, DNA-directed RNA polymerase |
#9: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P38902, DNA-directed RNA polymerase |
-DNA-directed RNA polymerases I, II, and III ... , 5 types, 5 molecules EFHJL
#4: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20434, DNA-directed RNA polymerase |
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#5: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20435, DNA-directed RNA polymerase |
#6: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20436, DNA-directed RNA polymerase |
#8: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P22139, DNA-directed RNA polymerase |
#10: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P40422, DNA-directed RNA polymerase |
-Protein , 1 types, 1 molecules M
#11: Protein | Mass: 7337.035 Da / Num. of mol.: 1 / Fragment: TFIIB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Sua7 / Plasmid: pTYB2-SUA7 / Production host: Escherichia coli (E. coli) / Strain (production host): Codon Plus Ril |
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-Non-polymers , 2 types, 10 molecules
#12: Chemical | ChemComp-ZN / #13: Chemical | ChemComp-MG / | |
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-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: 5.11 Å3/Da / Density % sol: 75.94 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate, MES, NaCl, CdCl2, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, sitting drop / Details: A.L., Gnatt, (2001) Science, 292, 1876. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.998 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.998 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→50 Å / Num. obs: 57906 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rsym value: 0.091 / Net I/σ(I): 14 |
Reflection shell | Resolution: 4.5→4.7 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.277 / % possible all: 99.2 |
Reflection | *PLUS Rmerge(I) obs: 0.091 |
Reflection shell | *PLUS % possible obs: 99.2 % / Num. unique obs: 8951 / Rmerge(I) obs: 0.277 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I6H Resolution: 4.5→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 150.99 Å2
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Refinement step | Cycle: LAST / Resolution: 4.5→50 Å
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Refine LS restraints |
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