Alpha-amanitin inhibited complete RNA polymerase II elongation complex
DOI:10.2210/pdb2vum/pdb   NDB ID: 2VUM
2VUM
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/toxin
    Structure Weight: 531506.25
    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
    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 SUBUNIT RPB4
    Polymer: 4 Type: protein Length: 221
    Chains: D
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB4 YJL140W J0654
    UniProtKB: Protein Feature View | Search PDB | P20433  
    Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
    Polymer: 5 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 POLYMERASES I, II, AND III SUBUNIT RPABC2
    Polymer: 6 Type: protein Length: 155
    Chains: F
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
    Polymer: 7 Type: protein Length: 171
    Chains: G
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPB7 YDR404C D9509.22
    UniProtKB: Protein Feature View | Search PDB | P34087  
    Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
    Polymer: 8 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 SUBUNIT RPB9
    Polymer: 9 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 POLYMERASES I, II, AND III SUBUNIT RPABC5
    Polymer: 10 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 SUBUNIT RPB11
    Polymer: 11 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 POLYMERASES I, II, AND III SUBUNIT RPABC4
    Polymer: 12 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: 13 Type: protein Length: 8
    Chains: M
    Organism: Amanita phalloides
    Molecule: 5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3'
    Polymer: 14 Type: dna Length: 14
    Chains: N
    Molecule: 5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'
    Polymer: 15 Type: rna Length: 11
    Chains: P
    Molecule: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *GP*TP*TP*AP*CP*GP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'
    Polymer: 16 Type: dna Length: 26
    Chains: T
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 2
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 3
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 4
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 5
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 6
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 7
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 8
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 9
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 10
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 11
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 12
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast  
    Polymer: 13
    Scientific Name: Amanita phalloides   Taxonomy   Common Name: Death cap  
    Polymer: 14
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 15
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 16
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1A1D   YEAST RIBONUCLEIC ACID POLYMERASE SUBUNIT RPB8, NMR, MINIMIZED AVERAGE STRUCTURE, ALPHA CARBONS ONLY 
    1DZF   RPB5 FROM S.CEREVISIAE 
    1I3Q   RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION 
    1I50   RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION 
    1I6H   RNA POLYMERASE II ELONGATION COMPLEX 
    1K83   CRYSTAL STRUCTURE OF YEAST RNA POLYMERASE II COMPLEXED WITH THE INHIBITOR ALPHA-AMANITIN 
    1NIK   WILD TYPE RNA POLYMERASE II 
    1NT9   COMPLETE 12-SUBUNIT RNA POLYMERASE II 
    1PQV   RNA POLYMERASE II-TFIIS COMPLEX 
    1R5U   RNA POLYMERASE II TFIIB COMPLEX 
    1R9S   RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX,MATCHED NUCLEOTIDE 
    1R9T   RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE 
    1SFO   RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX 
    1TWA   RNA POLYMERASE II COMPLEXED WITH ATP 
    1TWC   RNA POLYMERASE II COMPLEXED WITH GTP 
    1TWF   RNA POLYMERASE II COMPLEXED WITH UTP AT 2.3 A RESOLUTION 
    1TWG   RNA POLYMERASE II COMPLEXED WITH CTP 
    1TWH   RNA POLYMERASE II COMPLEXED WITH 2'DATP 
    1WCM   COMPLETE 12-SUBUNIT RNA POLYMERASE II AT 3.8 A 
    1Y14   CRYSTAL STRUCTURE OF YEAST SUBCOMPLEX OF RPB4 AND RPB7 
    1Y1V   REFINED RNA POLYMERASE II-TFIIS COMPLEX 
    1Y1W   COMPLETE RNA POLYMERASE II ELONGATION COMPLEX 
    1Y1Y   RNA POLYMERASE II-TFIIS-DNA/RNA COMPLEX 
    1Y77   COMPLETE RNA POLYMERASE II ELONGATION COMPLEX WITHSUBSTRATE ANALOGUE GMPCPP 
    2B63   COMPLETE RNA POLYMERASE II-RNA INHIBITOR COMPLEX 
    2B8K   12-SUBUNIT RNA POLYMERASE II 
    2JA5   CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX A 
    2JA6   CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX B 
    2JA7   CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX C 
    2JA8   CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX D 
    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
    MG
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    MG Mg
    MAGNESIUM 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
    BRU
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    BRU C9 H12 Br N2 O8 P DU dnaLinking
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:2VUM
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Brueckner, F.,  Cramer, P.

    Deposition:   2008-05-27
    Release:   2008-06-17
    Last Modified (REVDAT):   2011-07-13
     
  •   Revision History    Hide
    Mouse over text for details
    2012-12-12
    Other
    2011-07-13
    Atom nomenclature
    2011-07-13
    Binding sites and description
    2011-07-13
    Polymer description
    2011-07-13
    Version format compliance
    2011-07-13
    Linkage
    2011-07-13
    Sequence database correspondence
    2011-07-13
    Function and keywords
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.40
    R-Value: 0.255 (obs.)
    R-Free: 0.288
    Space Group: C 2 2 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 220.62 α = 90.00 
    b = 394.23 β = 90.00 
    c = 283.97 γ = 90.00