+Open data
-Basic information
Entry | Database: PDB / ID: 1pqv | ||||||
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Title | RNA polymerase II-TFIIS complex | ||||||
Components |
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Keywords | TRANSFERASE/TRANSCRIPTION / TRANSCRIPTION / MRNA CLEAVAGE / PROOFREADING / BACKTRACKING / GENE EXPRESSION / MULTIPROTEIN COMPLEX / PROTEIN SOAKING / TRANSFERASE-TRANSCRIPTION 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: 3.8 Å | ||||||
Authors | Kettenberger, H. / Armache, K.-J. / Cramer, P. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Architecture of the RNA Polymerase II-TFIIS Complex and Implications for mRNA Cleavage Authors: Kettenberger, H. / Armache, K.-J. / Cramer, P. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Architecture of initiation-competent 12-subunit RNA polymerase II Authors: Armache, K.-J. / Kettenberger, H. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pqv.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pqv.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 1pqv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pqv_validation.pdf.gz | 411.3 KB | Display | wwPDB validaton report |
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Full document | 1pqv_full_validation.pdf.gz | 411.6 KB | Display | |
Data in XML | 1pqv_validation.xml.gz | 2 KB | Display | |
Data in CIF | 1pqv_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pqv ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pqv | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
#1: 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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#2: 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 |
#3: 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 |
#4: Protein | Mass: 24674.189 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 |
#7: 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 |
#9: 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 |
#11: 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 ... , 5 types, 5 molecules EFHJL
#5: 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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#6: 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 |
#8: 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 |
#10: 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 |
#12: 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 , 1 types, 1 molecules S
#13: Protein | Mass: 34903.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07273 |
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-Non-polymers , 2 types, 10 molecules
#14: Chemical | ChemComp-MG / |
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#15: Chemical | ChemComp-ZN / |
-Details
Sequence details | SEQUENCE Numbering of residues D86-D114 is arbitrary. |
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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: 5.54 Å3/Da / Density % sol: 77.81 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: sodium-ammonium tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 26, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. all: 115508 / Num. obs: 115508 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.089 |
Reflection shell | Resolution: 3.8→3.94 Å / Redundancy: 1.2 % / Num. unique all: 9618 / Rsym value: 0.355 / % possible all: 81 |
Reflection | *PLUS Highest resolution: 3.8 Å / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS Highest resolution: 3.8 Å / % possible obs: 81 % / Num. unique obs: 9618 / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→50 Å / σ(F): 0 / Details: No least square refinement has been performed. /
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Refinement step | Cycle: LAST / Resolution: 3.8→50 Å
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Refinement | *PLUS Highest resolution: 3.8 Å / Rfactor Rwork: 0.392 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |