Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin DOI:10.2210/pdb3cqz/pdb

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Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Transcription/toxin Structure Weight: 471090.15 Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 Polymer: 1 Type: protein Length: 1733 Chains: A EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPO21 RPB1 RPB220 SUA8 YDL140C D2150 UniProtKB:   Protein Feature View | Search PDB | P04050     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 Polymer: 2 Type: protein Length: 1224 Chains: B EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB2 RPB150 RPO22 YOR151C UniProtKB:   Protein Feature View | Search PDB | P08518     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 Polymer: 3 Type: protein Length: 318 Chains: C Organism Saccharomyces cerevisiae Gene Names RPB3 YIL021W UniProtKB:   Protein Feature View | Search PDB | P16370     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 Polymer: 4 Type: protein Length: 215 Chains: E Organism Saccharomyces cerevisiae Gene Names RPB5 RPA7 RPC9 YBR154C YBR1204 UniProtKB:   Protein Feature View | Search PDB | P20434     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 Polymer: 5 Type: protein Length: 155 Chains: F Organism Saccharomyces cerevisiae Gene Names RPO26 RPB6 YPR187W P9677.8 UniProtKB:   Protein Feature View | Search PDB | P20435     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 Polymer: 6 Type: protein Length: 146 Chains: H Organism Saccharomyces cerevisiae Gene Names RPB8 YOR224C YOR50-14 UniProtKB:   Protein Feature View | Search PDB | P20436     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 Polymer: 7 Type: protein Length: 122 Chains: I Organism Saccharomyces cerevisiae Gene Names RPB9 YGL070C UniProtKB:   Protein Feature View | Search PDB | P27999     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 Polymer: 8 Type: protein Length: 70 Chains: J Organism Saccharomyces cerevisiae Gene Names RPB10 YOR210W UniProtKB:   Protein Feature View | Search PDB | P22139     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 Polymer: 9 Type: protein Length: 120 Chains: K Organism Saccharomyces cerevisiae Gene Names RPB11 YOL005C UniProtKB:   Protein Feature View | Search PDB | P38902     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 Polymer: 10 Type: protein Length: 70 Chains: L Organism Saccharomyces cerevisiae Gene Names RPC10 RPB12 YHR143W-A YHR143BW UniProtKB:   Protein Feature View | Search PDB | P40422     Molecule: ALPHA-AMANITIN Polymer: 11 Type: protein Length: 8 Chains: M Organism Amanita phalloides UniProtKB:   Protein Feature View | Search PDB | P85421         Source Hide Polymer: 1 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 2 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 3 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 4 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 5 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 6 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 7 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 8 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 9 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 10 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Brewer's yeast, lager beer yeast, yeast   Polymer: 11 Scientific Name: Synthetic construct (Amanita phalloides)   Taxonomy         Related PDB Entries Hide Identifier Details 1K83  CRYSTAL STRUCTURE OF A COMPLETE RNA POLYMERASE II ELONGATION COMPLEXED WITH THE INHIBITOR ALPHA-AMANITIN  2VUM  CRYSTAL STRUCTURE OF ALPHA-AMANITIN COMPLEXED WITH A COMPLETE RNA POLYMERASE II ELONGATION COMPLEX      Biologically Interesting Molecules (BIRD) Hide Identifier Image Name Type Class Chain ID   PRD_000201 Search  Alpha-Amanitin Cyclic peptide Toxin M   Ligand Explorer     Ligand Chemical Component Hide Identifier Formula Name Interactions ZN Search  Download  Zn ZINC ION   Ligand Explorer     Modified Residues Hide Identifier Formula Parent Type ILX Search  C6 H13 N O4 ILE lPeptideLinking TRX Search  C11 H12 N2 O3 TRP lPeptideLinking CSX Search  C3 H7 N O3 S CYS lPeptideLinking HYP Search  C5 H9 N O3 PRO lPeptideLinking     External Domain Annotations Hide SCOP Classification v1.75: 7 Domains - data from SCOP   CATH Classification v3.4.0: 11 Domains - data from CATH   Pfam Classification: 26 Domains - data from Pfam   GO Terms: 151 Terms - data from GO      Structural Biology Knowledgebase Data Hide     Data in orange boxes are gathered from external resources (when available). 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Biological Assembly            View in 3D More Images... Biological assembly 1 generated by PISA (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Kaplan, C.D.,  Larsson, K.-M.,  Kornberg, R.D. Deposition:   2008-04-03 Release:   2008-07-22 Last Modified (REVDAT):   2011-07-27     Revision History    Hide Mouse over text for details 2012-12-12 Other 2011-07-27 Binding sites and description 2011-07-27 Non-polymer description 2011-07-27 Function and keywords 2011-07-27 Other 2011-07-27 Linkage 2011-07-27 Sequence database correspondence 2011-07-27 Polymer description 2011-07-27 Flag residual B-value 2011-07-27 Atom nomenclature 2011-07-13 Version format compliance     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   2.80 R-Value: 0.202 (obs.) R-Free: 0.273 Space Group: I 2 2 2 Unit Cell:   Length [Å] Angles [°] a = 122.51 α = 90.00  b = 222.48 β = 90.00  c = 374.23 γ = 90.00      Molecule of the Month Hide RNA Polymerase