[English] 日本語
Yorodumi- PDB-2vum: Alpha-amanitin inhibited complete RNA polymerase II elongation complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vum | ||||||
---|---|---|---|---|---|---|---|
Title | Alpha-amanitin inhibited complete RNA polymerase II elongation complex | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / DNA-DIRECTED RNA POLYMERASE / ALPHA-AMANITIN / UBL CONJUGATION / NUCLEAR PROTEIN / RNA POLYMERASE II / ELONGATION COMPLEX / MRNA PROCESSING / PHOSPHORYLATION / ENZYME INHIBITION / DNA DAMAGE / DNA REPAIR / ZINC-FINGER / DNA-BINDING / TRANSFERASE/DNA/RNA / TRANSCRIPTION BUBBLE / ZINC / NUCLEUS / CYTOPLASM / INHIBITOR / MAGNESIUM / TRANSCRIPTION INHIBITION / TRANSLOCATION INTERMEDIATE / TRANSCRIPTION / METAL-BINDING / PHOSPHOPROTEIN / INTERMEDIATE / FUNGAL TOXIN / POLYMORPHISM / NUCLEOTIDYLTRANSFERASE / TRANSCRIPTION MECHANISM | ||||||
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 / RNA polymerase II activity / positive regulation of translational initiation / 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 / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / single-stranded DNA binding / ribosome biogenesis / toxin activity / 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) AMANITA PHALLOIDES (death cap) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Brueckner, F. / Cramer, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation. Authors: Brueckner, F. / Cramer, P. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vum.cif.gz | 835.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vum.ent.gz | 654.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/2vum ftp://data.pdbj.org/pub/pdb/validation_reports/vu/2vum | HTTPS FTP |
---|
-Related structure data
Related structure data | 1y1wS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#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: 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 |
#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 |
---|---|
#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 chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 4263.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others) |
---|---|
#16: DNA chain | Mass: 8043.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others) |
-Protein/peptide / RNA chain , 2 types, 2 molecules MP
#13: Protein/peptide | Mass: 939.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) AMANITA PHALLOIDES (death cap) / References: UniProt: P85421 |
---|---|
#15: RNA chain | Mass: 3552.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 9 molecules
#17: Chemical | ChemComp-ZN / #18: Chemical | ChemComp-MG / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.83 Å3/Da / Density % sol: 81.2 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 200 MM AMMONIUM ACETATE, 300 MM SODIUM ACETATE, 50 MM HEPES PH 7.0, 4-7% PEG 6000, 5 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91901 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91901 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 328642 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y1W Resolution: 3.4→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Bsol: 49.4797 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|