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Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin
1K83
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transcription/toxin
    Structure Weight: 471145.09
    Molecule: DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
    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 140KD POLYPEPTIDE
    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 45KD POLYPEPTIDE
    Polymer: 3 Type: protein Length: 318
    Chains: C
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB3 YIL021W
    UniProtKB: Protein Feature View | Search PDB | P16370  
    Molecule: DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDE
    Polymer: 4 Type: protein Length: 215
    Chains: E
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB5 RPA7 RPC9 YBR154C YBR1204
    UniProtKB: Protein Feature View | Search PDB | P20434  
    Molecule: DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDE
    Polymer: 5 Type: protein Length: 155
    Chains: F
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPO26 RPB6 YPR187W P9677.8
    UniProtKB: Protein Feature View | Search PDB | P20435  
    Molecule: DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDE
    Polymer: 6 Type: protein Length: 146
    Chains: H
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB8 YOR224C YOR50-14
    UniProtKB: Protein Feature View | Search PDB | P20436  
    Molecule: DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE
    Polymer: 7 Type: protein Length: 122
    Chains: I
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB9 YGL070C
    UniProtKB: Protein Feature View | Search PDB | P27999  
    Molecule: DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDE
    Polymer: 8 Type: protein Length: 70
    Chains: J
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB10 YOR210W
    UniProtKB: Protein Feature View | Search PDB | P22139  
    Molecule: DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE
    Polymer: 9 Type: protein Length: 120
    Chains: K
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB11 YOL005C
    UniProtKB: Protein Feature View | Search PDB | P38902  
    Molecule: DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDE
    Polymer: 10 Type: protein Length: 70
    Chains: L
    EC#: 2.7.7.6   
    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  
     
  •   Structure Validation Hide

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  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 2
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 3
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 4
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 5
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 6
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 7
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 8
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 9
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 10
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 11
    Scientific Name: Amanita phalloides   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1I50  YEAST RNA POLYMERASE II AT 2.8 ANGSTROMS 
    2VUM  CRYSTAL STRUCTURE OF A COMPLETE RNA POLYMERASE II ELONGATION COMPLEXED WITH THE INHIBITOR ALPHA-AMANITIN 
    3CQZ  CRYSTAL STRUCTURE OF 10 SUBUNIT RNA POLYMERASE II COMPLEXED WITH THE INHIBITOR ALPHA-AMANITIN 
     
  •   Biologically Interesting Molecules (BIRD) Hide
    Identifier Image Name Type Class Chain ID  
    PRD_000201 Search  PRD_000201 Alpha-Amanitin Cyclic peptide Toxin M
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    MN
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    Download 
    MN Mn
    MANGANESE (II) ION
    ZN
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    ZN Zn
    ZINC ION
     
  •   Modified Residues Hide
    Identifier Formula Parent Type
    ILX
    Search 
    ILX C6 H13 N O4 ILE lPeptideLinking
    TRX
    Search 
    TRX C11 H12 N2 O3 TRP lPeptideLinking
    CSX
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    CSX C3 H7 N O3 S CYS lPeptideLinking
    HYP
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    HYP C5 H9 N O3 PRO lPeptideLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors
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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Bushnell, D.A.,  Cramer, P.,  Kornberg, R.D.

    Deposition:   2001-10-22
    Release:   2002-02-13
    Last Modified (REVDAT):   2011-07-27
     
  •   Revision History    Hide
    Mouse over text for details
    2012-12-12
    Other
    2011-07-27
    Linkage
    2011-07-27
    Sequence database correspondence
    2011-07-27
    Polymer description
    2011-07-27
    Atom nomenclature
    2011-07-27
    Binding sites and description
    2011-07-27
    Non-polymer description
    2011-07-27
    Function and keywords
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.80
    R-Value: 0.229 (obs.)
    R-Free: 0.280
    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