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Open data
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Basic information
Entry | Database: PDB / ID: 3gtq | ||||||
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Title | Backtracked RNA polymerase II complex induced by damage | ||||||
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![]() | TRANSCRIPTION / TRANSFERASE/DNA-RNA HYBRID / TRANSFERASE / DNA-RNA HYBRID / Backtrack / DNA-directed RNA polymerase / DNA binding / Isopeptide bond / Magnesium / Metal binding / Nucleotidyltransferase / Nucleus / Phosphoprotein / Zinc-finger / DNA damage / DNA repair / TRANSFERASE-DNA-RNA HYBRID COMPLEX | ||||||
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 / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase II transcription / 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 III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / Formation of TC-NER Pre-Incision Complex / : / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / transcription by RNA polymerase III / translesion synthesis / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / : / : / : / : / : / : / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / DNA-directed RNA polymerase activity / ribonucleoside binding / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D. | ||||||
![]() | ![]() Title: Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution. Authors: Wang, D. / Bushnell, D.A. / Huang, X. / Westover, K.D. / Levitt, M. / Kornberg, R.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 739.9 KB | Display | ![]() |
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PDB format | ![]() | 578.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 583.6 KB | Display | ![]() |
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Full document | ![]() | 779.4 KB | Display | |
Data in XML | ![]() | 139.1 KB | Display | |
Data in CIF | ![]() | 190.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gtgC ![]() 3gtjC ![]() 3gtkC ![]() 3gtlC ![]() 3gtmC ![]() 3gtoC ![]() 3gtpC ![]() 1r9tS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | ASYMMETRIC UNIT IS THE BIOLOGICAL UNIT |
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Components
-DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II largest subunit / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerase II 140 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 35330.457 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II 45 kDa polypeptide / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerase II subunit 9 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 13633.493 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerase II 13.6 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#4: Protein | Mass: 25117.094 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#5: Protein | Mass: 17931.834 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#6: Protein | Mass: 16525.363 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Fragment: DNA-directed RNA polymerases I/II/III subunit 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 7729.969 Da / Num. of mol.: 1 Fragment: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain / DNA chain / Non-polymers , 3 types, 10 molecules RT

#11: RNA chain | Mass: 3914.424 Da / Num. of mol.: 1 / Fragment: RNA strand / Source method: obtained synthetically / Details: Synthetic RNA |
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#12: DNA chain | Mass: 8679.603 Da / Num. of mol.: 1 / Fragment: DNA template strand / Source method: obtained synthetically / Details: Synthetic template DNA |
#13: Chemical | ChemComp-ZN / |
-Details
Has protein modification | Y |
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Sequence details | THE DNA NON-TEMPLATE STRAND (LABELED AS ENTITY 13 IN THE RELATED ENTRIES) IS MISSING IN COORDINATES ...THE DNA NON-TEMPLATE STRAND (LABELED AS ENTITY 13 IN THE RELATED ENTRIES) IS MISSING IN COORDINATE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.61 Å3/Da / Density % sol: 65.95 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. obs: 66377 / % possible obs: 96.1 % / Redundancy: 2.7 % / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1R9T Resolution: 3.8→50 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.821 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.896 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTIRE CHAIN N WHICH IS A DNA NON-TEMPLATE STRAND, REPORTED AS ENTITY 13 IN RELATED ENTRIES WITH THE SEQUENCE (DG)(DT)(DG)(DG)(DT)(DT) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ENTIRE CHAIN N WHICH IS A DNA NON-TEMPLATE STRAND, REPORTED AS ENTITY 13 IN RELATED ENTRIES WITH THE SEQUENCE (DG)(DT)(DG)(DG)(DT)(DT)(DA)(DT)(DG)(DG)(DG)(DT)(DA)(DG), IS MISSING IN COORDINATES DUE TO LACK OF ELECTRON DENSITY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 95.463 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.8→3.9 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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