+Open data
-Basic information
Entry | Database: PDB / ID: 2b63 | ||||||
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Title | Complete RNA Polymerase II-RNA inhibitor complex | ||||||
Components |
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Keywords | TRANsferase/RNA / RNA Polymerase II / RNA / aptamer / protein-RNA complex / inhibitor / TRANsferase-RNA COMPLEX | ||||||
Function / homology | Function and homology information 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 / termination of RNA polymerase II transcription / 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 / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / translation initiation factor binding / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / ribosome biogenesis / peroxisome / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / mRNA binding / nucleotide binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å | ||||||
Authors | Kettenberger, H. / Eisenfuehr, A. / Brueckner, F. / Theis, M. / Famulok, M. / Cramer, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2006 Title: Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs Authors: Kettenberger, H. / Eisenfuehr, A. / Brueckner, F. / Theis, M. / Famulok, M. / Cramer, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b63.cif.gz | 827.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b63.ent.gz | 646.8 KB | Display | PDB format |
PDBx/mmJSON format | 2b63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b63_validation.pdf.gz | 605.2 KB | Display | wwPDB validaton report |
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Full document | 2b63_full_validation.pdf.gz | 891.3 KB | Display | |
Data in XML | 2b63_validation.xml.gz | 168 KB | Display | |
Data in CIF | 2b63_validation.cif.gz | 229.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/2b63 ftp://data.pdbj.org/pub/pdb/validation_reports/b6/2b63 | HTTPS FTP |
-Related structure data
Related structure data | 1wcmS S: Starting model for refinement |
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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 ... , 7 types, 7 molecules ABCDGIK
#2: 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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#3: 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 |
#4: Protein | Mass: 35330.457 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 |
#5: Protein | Mass: 25451.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB4 / Production host: Escherichia coli (E. coli) / References: UniProt: P20433, DNA-directed RNA polymerase |
#8: Protein | Mass: 19081.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P34087, DNA-directed RNA polymerase |
#10: 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 |
#12: 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 ... , 4 types, 4 molecules EFHL
#6: 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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#7: 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 |
#9: 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 |
#13: 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 |
-RNA chain / Protein , 2 types, 2 molecules RJ
#11: 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 |
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#1: RNA chain | Mass: 10323.542 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: synthetic oligonucleotide containing four 5-bromo-uridine (5BU) residues |
-Non-polymers , 2 types, 9 molecules
#14: Chemical | ChemComp-ZN / #15: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 6.133201 Å3/Da / Density % sol: 79.945221 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Details: 200 mM ammonium acetate, 150 mM magnesium acetate, 50 mM Hepes (pH 7.0), 5% PEG 6000, and 5 mM TCEP | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9189 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 22, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9189 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. all: 248494 / Num. obs: 248494 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1WCM Resolution: 3.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Anomalous data were collected and used to calculate anomalous Fourier maps and for refinement. Residues 22-25 of chain R were excluded from refinement due to a high degree of disorder. The ...Details: Anomalous data were collected and used to calculate anomalous Fourier maps and for refinement. Residues 22-25 of chain R were excluded from refinement due to a high degree of disorder. The occupancies for these residues are zero.
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Solvent computation | Bsol: 11.985 Å2 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.434 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→50 Å
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Xplor file |
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