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Yorodumi- PDB-3hoz: Complete RNA polymerase II elongation complex IV with a T-U misma... -
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-Basic information
Entry | Database: PDB / ID: 3hoz | ||||||
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Title | Complete RNA polymerase II elongation complex IV with a T-U mismatch and a frayed RNA 3'-guanine | ||||||
Components |
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Keywords | TRANSCRIPTION / TRANSFERASE/DNA/RNA HYBRID / RNA-FRAYING / RNA POLYMERASE II / METAL BINDING / TRANSCRIPTION BUBBLE / ELONGATION COMPLEX / DNA-RNA MISMATCH / RNA fraying / DNA-binding / DNA-directed RNA polymerase / Isopeptide bond / Magnesium / Nucleotidyltransferase / Nucleus / Phosphoprotein / Transferase / Ubl conjugation / Zinc / Zinc-finger / Polymorphism / Cytoplasm / DNA damage / DNA repair / mRNA processing / TRANSFERASE-DNA-RNA HYBRID COMPLEX | ||||||
Function / homology | Function and homology information RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 ...RPB4-RPB7 complex / : / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / 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 / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / translesion synthesis / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / peroxisome / single-stranded DNA binding / ribosome biogenesis / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å | ||||||
Authors | Sydow, J.F. / Brueckner, F. / Cheung, A.C.M. / Damsma, G.E. / Dengl, S. / Lehmann, E. / Vassylyev, D. / Cramer, P. | ||||||
Citation | Journal: Mol.Cell / Year: 2009 Title: Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA. Authors: Sydow, J.F. / Brueckner, F. / Cheung, A.C.M. / Damsma, G.E. / Dengl, S. / Lehmann, E. / Vassylyev, D. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hoz.cif.gz | 831.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hoz.ent.gz | 649.3 KB | Display | PDB format |
PDBx/mmJSON format | 3hoz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/3hoz ftp://data.pdbj.org/pub/pdb/validation_reports/ho/3hoz | HTTPS FTP |
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-Related structure data
Related structure data | 3houSC 3hovC 3howC 3hoxC 3hoyC S: Starting model for refinement C: citing same article (ref.) |
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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 subunit ... , 7 types, 7 molecules ABCDGIK
#1: Protein | Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase |
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#2: Protein | Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase |
#3: Protein | Mass: 38677.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P16370, DNA-directed RNA polymerase |
#4: Protein | Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase |
#7: Protein | Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34087, 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) / References: UniProt: P27999, 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) / References: UniProt: P38902, DNA-directed RNA polymerase |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434, DNA-directed RNA polymerase |
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#6: Protein | Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / 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) / References: UniProt: P20436, 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) / References: UniProt: P22139, 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) / References: UniProt: P40422, DNA-directed RNA polymerase |
-DNA chain , 2 types, 2 molecules NT
#13: DNA chain | Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#14: DNA chain | Mass: 8034.007 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-RNA chain , 1 types, 1 molecules P
#15: RNA chain | Mass: 5709.428 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Non-polymers , 2 types, 9 molecules
#16: Chemical | ChemComp-ZN / #17: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.74 Å3/Da / Density % sol: 78.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20mM ammonium acetate, 300mM SODIUM ACETATE, 50mM Hepes pH 7.0, 4-6% PEG 6000, 5mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9188 Å / Relative weight: 1 |
Reflection | Resolution: 3.65→50 Å / Num. all: 135977 / Num. obs: 135977 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.077 / Net I/σ(I): 22 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HOU Resolution: 3.65→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.65→50 Å
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