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Open data
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Basic information
Entry | Database: PDB / ID: 1i3q | |||||||||
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Title | RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION | |||||||||
![]() | (DNA-DIRECTED RNA POLYMERASE II ...) x 10 | |||||||||
![]() | TRANSCRIPTION / mRNA / multiprotein complex / molecular machine / zinc motifs | |||||||||
Function / homology | ![]() 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 / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...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 / 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 / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / 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 / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cramer, P. / Bushnell, D.A. / Kornberg, R.D. | |||||||||
![]() | ![]() Title: Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Authors: Cramer, P. / Bushnell, D.A. / Kornberg, R.D. #1: ![]() 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 inspecition, see primary citation. | |||||||||
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 inspecition, see primary citation. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 715.9 KB | Display | ![]() |
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PDB format | ![]() | 569.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.1 KB | Display | ![]() |
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Full document | ![]() | 678.1 KB | Display | |
Data in XML | ![]() | 94.3 KB | Display | |
Data in CIF | ![]() | 138.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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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
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 2 types, 9 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#11: Chemical | ChemComp-ZN / #12: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, Ammoniumhydrogenphosphate, Sodiumdihydrogenphosphate, dioxane, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: Fu, J., (1999) Cell, 98, 799. / 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 26, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.283 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→40 Å / Num. obs: 98315 / % possible obs: 99.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 3.1→3.2 Å / Rmerge(I) obs: 0.298 / Num. unique all: 9073 / % possible all: 92.7 |
Reflection | *PLUS Lowest resolution: 40 Å |
Reflection shell | *PLUS % possible obs: 92.7 % / Num. unique obs: 9073 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 71.5 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→40 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 40 Å / σ(F): 0 / Rfactor obs: 0.229 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 71.5 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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