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Yorodumi- PDB-2r92: Elongation complex of RNA polymerase II with artificial RdRP scaffold -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r92 | ||||||
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Title | Elongation complex of RNA polymerase II with artificial RdRP scaffold | ||||||
Components |
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Keywords | Transferase/RNA / TRANSFERASE/DNA/RNA / DNA-BINDING / PHOSPHORYLATION / RNA POLYMERASE II / METAL-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION BUBBLE / ELONGATION COMPLEX / TRANSFERASE / TRANSCRIPTION / RNA-DEPENDENT / RNA-DEPENDENT RNA SYNTHESIS / RDRP / DDRP / RNA-BINDING / DNA-directed RNA polymerase / Magnesium / Nucleotidyltransferase / Nucleus / Ubl conjugation / Zinc / Zinc-finger / Polymorphism / Cytoplasm / DNA damage / DNA repair / mRNA processing / Transferase-RNA COMPLEX | ||||||
Function / homology | Function and homology information RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / 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 / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / translation initiation factor binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / ribosome biogenesis / peroxisome / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / mRNA binding / nucleotide 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: 3.8 Å | ||||||
Authors | Lehmann, E. / Brueckner, F. / Cramer, P. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Molecular basis of RNA-dependent RNA polymerase II activity. Authors: Lehmann, E. / Brueckner, F. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r92.cif.gz | 813.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r92.ent.gz | 652.9 KB | Display | PDB format |
PDBx/mmJSON format | 2r92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r92_validation.pdf.gz | 600 KB | Display | wwPDB validaton report |
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Full document | 2r92_full_validation.pdf.gz | 917.4 KB | Display | |
Data in XML | 2r92_validation.xml.gz | 172.5 KB | Display | |
Data in CIF | 2r92_validation.cif.gz | 233.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/2r92 ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r92 | 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
-RNA chain , 2 types, 2 molecules PT
#1: RNA chain | Mass: 5144.159 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 5403.261 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules ABCDGIK
#3: 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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#4: 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 |
#5: 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 |
#6: 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 |
#9: 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 |
#11: 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 |
#13: 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
#7: 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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#8: 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 |
#10: 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 |
#12: 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 |
#14: 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 |
-Non-polymers , 2 types, 9 molecules
#15: Chemical | ChemComp-ZN / #16: 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: 5.92 Å3/Da / Density % sol: 79.24 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / pH: 7 Details: 5% (w/v) PEG 6000, 200 mM ammonium acetate, 150 mM magnesium acetate, 50 mM Hepes pH 7.0, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.07158 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07158 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 122098 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rsym value: 0.077 / Net I/σ(I): 21.38 |
Reflection shell | Resolution: 3.8→3.94 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 6.77 / Rsym value: 0.335 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 3.8→50 Å
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Refine LS restraints |
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