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Yorodumi- PDB-5c4j: Crystal structure of a transcribing RNA Polymerase II complex rev... -
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-Basic information
Entry | Database: PDB / ID: 5c4j | ||||||
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Title | Crystal structure of a transcribing RNA Polymerase II complex reveals a complete transcription bubble | ||||||
Components |
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Keywords | TRANSFERASE/DNA/RNA / protein-DNA complex / RNA Polymerase II / transcribing complex / transcription bubble / TRANSFERASE-DNA-RNA 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 / 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-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / 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 / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / 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 / ribosome biogenesis / peroxisome / nucleic acid binding / transcription by RNA polymerase II / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Barnes, C.O. / Calero, M. / Malik, I. / Spahr, H. / Zhang, Q. / Pullara, F. / Kaplan, C.D. / Calero, G. | ||||||
Citation | Journal: Mol.Cell / Year: 2015 Title: Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Authors: Barnes, C.O. / Calero, M. / Malik, I. / Graham, B.W. / Spahr, H. / Lin, G. / Cohen, A.E. / Brown, I.S. / Zhang, Q. / Pullara, F. / Trakselis, M.A. / Kaplan, C.D. / Calero, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c4j.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5c4j.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 5c4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c4j_validation.pdf.gz | 568.1 KB | Display | wwPDB validaton report |
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Full document | 5c4j_full_validation.pdf.gz | 689 KB | Display | |
Data in XML | 5c4j_validation.xml.gz | 135 KB | Display | |
Data in CIF | 5c4j_validation.cif.gz | 183.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/5c4j ftp://data.pdbj.org/pub/pdb/validation_reports/c4/5c4j | HTTPS FTP |
-Related 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 natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / 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 (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P16370 |
#7: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P27999 |
#9: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / 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 natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P20434 |
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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 (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P20435 |
#6: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P20436 |
#8: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P22139 |
#10: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40422 |
-RNA chain , 1 types, 1 molecules R
#11: RNA chain | Mass: 2934.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-DNA chain , 2 types, 2 molecules SU
#12: DNA chain | Mass: 16395.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#13: DNA chain | Mass: 16191.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 10 molecules
#14: Chemical | ChemComp-ZN / #15: Chemical | ChemComp-MG / | |
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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: 4.81 Å3/Da / Density % sol: 74.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 4000, SODIUM MALONATE, HEPES, DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 4→174.08 Å / Num. all: 80485 / Num. obs: 80485 / % possible obs: 97 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 4→4.104 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.7 / % possible all: 96.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→174.08 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 115.986 / SU ML: 0.619 / Cross valid method: THROUGHOUT / ESU R Free: 0.701 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 231.032 Å2
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Refinement step | Cycle: LAST / Resolution: 4→174.08 Å
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