+Open data
-Basic information
Entry | Database: PDB / ID: 1i6h | ||||||
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Title | RNA POLYMERASE II ELONGATION COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA-RNA HYBRID / TRANSCRIPTION / MRNA / MULTIPROTEIN COMPLEX / MOLECULAR MACHINE / DNA / TRANSCRIPTION-DNA-RNA COMPLEX / TRANSCRIPTION-DNA-RNA HYBRID 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 Polymerase II Pre-transcription Events / RNA-templated transcription / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase I activity / RNA polymerase III complex / translesion synthesis / RNA polymerase II, core complex / 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 / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Gnatt, A.L. / Cramer, P. / Kornberg, R.D. | ||||||
Citation | Journal: Science / Year: 2001 Title: Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Authors: Gnatt, A.L. / Cramer, P. / Fu, J. / Bushnell, D.A. / Kornberg, R.D. #1: Journal: Science / Year: 2001 Title: Structural Basis of Transcription: RNA Polymerase II at 2.8 A Resolution Authors: Cramer, P. / Bushnell, D.A. / Kornberg, R.D. #2: Journal: Science / Year: 2000 Title: Architecture of RNA Polymerase II and Implications for the Transcription Mechanism Authors: Cramer, P. / Bushnell, D.A. / Fu, J. / Gnatt, A.L. / Maier-Davis, B. / Thompson, N.E. / Burgess, R.R. / Edwards, A.M. / David, P.R. / Kornberg, R.D. | ||||||
History |
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Remark 650 | HELIX REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was ...HELIX REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was assigned by visual inspection, see reference 1. | ||||||
Remark 700 | SHEET REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was ...SHEET REMOVAL OF THE SECONDARY STRUCTURE WAS REQUESTED BY THE AUTHOR. Secondary structure was assigned by visual inspection, see reference 1. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i6h.cif.gz | 737.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i6h.ent.gz | 577.6 KB | Display | PDB format |
PDBx/mmJSON format | 1i6h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i6h_validation.pdf.gz | 502.6 KB | Display | wwPDB validaton report |
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Full document | 1i6h_full_validation.pdf.gz | 740.4 KB | Display | |
Data in XML | 1i6h_validation.xml.gz | 100.1 KB | Display | |
Data in CIF | 1i6h_validation.cif.gz | 148.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/1i6h ftp://data.pdbj.org/pub/pdb/validation_reports/i6/1i6h | HTTPS FTP |
-Related structure data
Related structure data | 1i3qS S: Starting model for refinement |
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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-DIRECTED RNA POLYMERASE II ... , 10 types, 10 molecules ABCEFHIJKL
#3: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / 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) / Strain: DELTA-RPB4 / 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) / Strain: DELTA-RPB4 / References: UniProt: P16370, DNA-directed RNA polymerase |
#6: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20434, DNA-directed RNA polymerase |
#7: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: DELTA-RPB4 / 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) / Strain: DELTA-RPB4 / References: UniProt: P20436, 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) / Strain: DELTA-RPB4 / References: UniProt: P27999, 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) / Strain: DELTA-RPB4 / References: UniProt: P22139, 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) / Strain: DELTA-RPB4 / References: UniProt: P38902, 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) / Strain: DELTA-RPB4 / References: UniProt: P40422, DNA-directed RNA polymerase |
-DNA chain / RNA chain , 2 types, 2 molecules DR
#1: DNA chain | Mass: 3966.596 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TEMPLATE Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) |
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#2: RNA chain | Mass: 2893.823 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: The RNA was synthesized by the polymerase before the crystal was formed. |
-Non-polymers , 2 types, 9 molecules
#13: Chemical | ChemComp-MG / |
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#14: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.37 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 6 Details: PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 100K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.998 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.998 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→40 Å / Num. obs: 96867 / % possible obs: 100 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.111 |
Reflection shell | Resolution: 3.3→3.4 Å / Rmerge(I) obs: 0.317 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I3Q Resolution: 3.3→40 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 63.51 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→40 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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