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Open data
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Basic information
Entry | Database: PDB / ID: 3gtm | |||||||||
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Title | Co-complex of Backtracked RNA polymerase II with TFIIS | |||||||||
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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 / Ubl conjugation / Zinc / Zinc-finger / Polymorphism / Cytoplasm / DNA damage / DNA repair / Transcription regulation / TRANSFERASE-DNA-RNA HYBRID COMPLEX | |||||||||
Function / homology | ![]() RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / 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 complex recruiting activity / regulation of mRNA 3'-end processing / 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 / RNA polymerase II complex binding / 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 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / 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 antitermination / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / DNA-templated transcription / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
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 | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.2 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 595.2 KB | Display | ![]() |
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Full document | ![]() | 752.5 KB | Display | |
Data in XML | ![]() | 142.7 KB | Display | |
Data in CIF | ![]() | 192.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gtgC ![]() 3gtjC ![]() 3gtkC ![]() 3gtlC ![]() 3gtoC ![]() 3gtpC ![]() 3gtqC ![]() 1y1vS 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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P04050, DNA-directed RNA polymerase |
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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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P08518, DNA-directed RNA polymerase |
#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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P16370 |
#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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P27999 |
#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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P38902 |
-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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P20434 |
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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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P20435 |
#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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P20436 |
#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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P22139 |
#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) ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40422 |
-DNA chain , 2 types, 2 molecules NO
#13: DNA chain | Mass: 8534.519 Da / Num. of mol.: 1 / Fragment: DNA template strand / Source method: obtained synthetically / Details: Synthetic template DNA / Source: (synth.) synthetic construct (others) |
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#14: DNA chain | Mass: 4286.789 Da / Num. of mol.: 1 / Fragment: DNA non-template strand / Source method: obtained synthetically / Details: Synthetic non-template DNA / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain , 2 types, 2 molecules SM
#11: Protein | Mass: 19732.430 Da / Num. of mol.: 1 Fragment: Transcription Factor IIS E291H mutation, UNP residues 147-309 Mutation: E291H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: DST1, PPR2, YGL043W / Production host: ![]() ![]() |
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#12: RNA chain | Mass: 4220.589 Da / Num. of mol.: 1 / Fragment: RNA strand / Source method: obtained synthetically / Details: Synthetic RNA / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 10 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#15: Chemical | ChemComp-MG / |
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#16: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.32 % | ||||||||||||||||||||||||||||||||||||
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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: Mar 24, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→40 Å / Num. obs: 65617 / % possible obs: 94.8 % / Redundancy: 2 % / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.7 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1Y1V Resolution: 3.8→40 Å
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Refinement step | Cycle: LAST / Resolution: 3.8→40 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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