+Open data
-Basic information
Entry | Database: PDB / ID: 1y1y | ||||||
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Title | RNA Polymerase II-TFIIS-DNA/RNA complex | ||||||
Components |
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Keywords | TRANSFERASE/TRANSCRIPTION/DNA-RNA HYBRID / RNA Polymerase II / TFIIS / nucleic acids / transcription / readthrough / TRANSFERASE-TRANSCRIPTION-DNA-RNA HYBRID COMPLEX | ||||||
Function / homology | Function and homology information RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / 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 complex recruiting activity / regulation of mRNA 3'-end processing / 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 / RNA polymerase II complex binding / 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 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / 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 / positive regulation of transcription elongation by RNA polymerase II / translation initiation factor binding / transcription antitermination / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / DNA-templated transcription / 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: 4 Å | ||||||
Authors | Cramer, P. / Kettenberger, H. / Armache, K.-J. | ||||||
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 | 1y1y.cif.gz | 179.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y1y.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 1y1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y1y_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 1y1y_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 1y1y_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 1y1y_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/1y1y ftp://data.pdbj.org/pub/pdb/validation_reports/y1/1y1y | 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 ... , 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 ... , 4 types, 4 molecules EFHL
#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 |
#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 |
-Protein , 2 types, 2 molecules JS
#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 |
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#15: Protein | Mass: 20271.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: DST1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P07273 |
-DNA chain / RNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 2073.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
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#2: RNA chain | Mass: 1279.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.71 Å3/Da / Density % sol: 78.47 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9919 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9919 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. all: 103460 / Num. obs: 103460 / % possible obs: 98.7 % / Observed criterion σ(F): 20.3 / Observed criterion σ(I): 20.3 / Redundancy: 4.3 % / Rsym value: 0.07 |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→50 Å / σ(F): 5.4 / Stereochemistry target values: Engh & Huber Details: The coordinates for only the alpha carbons and phosphorus atoms are present in the structure. The number of missing atoms was so much that remark 470 for the missing atoms list were removed.
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Refinement step | Cycle: LAST / Resolution: 4→50 Å
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