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- PDB-3h3v: Yeast RNAP II containing poly(A)-signal sequence in the active site -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h3v | ||||||
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Title | Yeast RNAP II containing poly(A)-signal sequence in the active site | ||||||
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![]() | TRANSFERASE/DNA/RNA / DNA-BINDING / PHOSPHORYLATION / RNA POLYMERASE II / METAL-BINDING / NUCLEAR PROTEIN / TRANSCRIPTION BUBBLE / ELONGATION COMPLEX / TRANSFERASE / TRANSCRIPTION / POLYADENYLATION / TERMINATION / DNA-directed RNA polymerase / Isopeptide bond / Magnesium / Nucleotidyltransferase / Nucleus / Phosphoprotein / Zinc-finger / DNA damage / DNA repair / mRNA processing / TRANSFERASE-DNA-RNA complex | ||||||
Function / homology | ![]() 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 ...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 / 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 / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / positive regulation of translational initiation / 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 / translation initiation factor binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / single-stranded DNA binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dengl, S. / Cramer, P. | ||||||
![]() | ![]() Title: Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro Authors: Dengl, S. / Cramer, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 826.8 KB | Display | ![]() |
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PDB format | ![]() | 643.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 606.9 KB | Display | ![]() |
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Full document | ![]() | 978.1 KB | Display | |
Data in XML | ![]() | 181.3 KB | Display | |
Data in CIF | ![]() | 244.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1y1wS 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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Components
-DNA-directed RNA polymerase II subunit ... , 7 types, 7 molecules BCDEHJL
#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: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#9: Protein | Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#11: Protein | Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules FGIKM
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#8: Protein | Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#12: Protein | Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-DNA chain , 2 types, 2 molecules NT
#13: DNA chain | Mass: 4255.778 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#15: DNA chain | Mass: 7968.149 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-RNA chain , 1 types, 1 molecules P
#14: RNA chain | Mass: 5067.064 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 2 types, 9 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MG.gif)
#16: Chemical | ChemComp-ZN / #17: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.82 Å3/Da / Density % sol: 78.87 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / pH: 7 Details: 200 mM ammonium acetate, 50mM HEPES pH 7.0, 4% polyethylene glycol 6000, 5mM TCEP (tris (2-carboxyethyl) phosphine hydrochloride), VAPOR DIFFUSION, HANGING DROP, temperature 295.0 K | ||||||||||||||||||||||||||||||||||||
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 225 mm CCD / Detector: CCD / Date: Apr 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918905 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. obs: 202368 / % possible obs: 99.9 % / Redundancy: 4.3 % / Rsym value: 0.106 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 4→4.25 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.516 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Y1W Resolution: 4→50 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 4→50 Å
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Refine LS restraints |
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Xplor file |
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