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Yorodumi- PDB-1y77: Complete RNA Polymerase II elongation complex with substrate anal... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y77 | ||||||
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Title | Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSFERASE/DNA-RNA HYBRID / substrate / NTP / elongation / TRANSFERASE-DNA-RNA HYBRID 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 / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | ||||||
Authors | Kettenberger, H. / Armache, K.-J. / Cramer, P. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Complete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS Authors: Kettenberger, H. / Armache, K.-J. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y77.cif.gz | 831.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y77.ent.gz | 649.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y77_validation.pdf.gz | 682.5 KB | Display | wwPDB validaton report |
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Full document | 1y77_full_validation.pdf.gz | 987.8 KB | Display | |
Data in XML | 1y77_validation.xml.gz | 173.3 KB | Display | |
Data in CIF | 1y77_validation.cif.gz | 236.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y77 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y77 | HTTPS FTP |
-Related structure data
Related structure data | 1y1vC 1y1wSC 1y1yC S: Starting model for refinement C: citing same article (ref.) |
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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 chain , 2 types, 2 molecules TN
#1: DNA chain | Mass: 5811.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
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#2: DNA chain | Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
-DNA-directed RNA polymerase II ... , 7 types, 7 molecules ABCDGIK
#4: 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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#5: 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 |
#6: 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 |
#7: 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 |
#10: 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 |
#12: 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 |
#14: 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 ... , 4 types, 4 molecules EFHL
#8: 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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#9: 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 |
#11: 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 |
#15: 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 |
-RNA chain / Protein , 2 types, 2 molecules PJ
#13: 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 |
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#3: RNA chain | Mass: 3223.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
-Non-polymers , 3 types, 10 molecules
#16: Chemical | ChemComp-ZN / #17: Chemical | ChemComp-MG / | #18: Chemical | ChemComp-G2P / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.9 Å3/Da / Density % sol: 79.16 % |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y1W Resolution: 4.5→50 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber Details: The peptide bond distance between ASN A 119 and GLU A 120 is slightly long. Because the deposited model was derived by rigid-body minimisation from a similar model.
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Refinement step | Cycle: LAST / Resolution: 4.5→50 Å
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