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RNA polymerase II elongation complex B
DOI:10.2210/pdb3m4o/pdb   NDB ID: NA0478
3M4O
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna RNA Hybrid
    Structure Weight: 486556.58
    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: RNA (5'-R(*AP*UP*GP*GP*AP*GP*AP*GP*GP*A)-3')
    Polymer: 11 Type: rna Length: 10
    Chains: R
    Molecule: DNA (28-MER)
    Polymer: 12 Type: dna Length: 28
    Chains: T
    Molecule: DNA (5'-D(P*GP*TP*GP*GP*TP*TP*AP*TP*GP*GP*GP*TP*AP*G)-3')
    Polymer: 13 Type: dna Length: 14
    Chains: N
     
  •   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: 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   Taxonomy    
    Polymer: 12
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 13
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    1R9T   
    2E2H   
    3CO3   
    3M3Y   
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    C7P
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    C7P C5 H11 Cl N3 Pt
    cis-diammine(pyridine)chloroplatinum(II)
    MG
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    MG Mg
    MAGNESIUM ION
    ZN
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    ZN Zn
    ZINC ION
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: NA0478
     
 
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:   Wang, D.,  Zhu, G.,  Huang, X.,  Lippard, S.J.

    Deposition:   2010-03-11
    Release:   2010-05-12
    Last Modified (REVDAT):   2010-06-09
     
  •   Revision History    Hide
    Mouse over text for details
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.57
    R-Value: 0.244 (obs.)
    R-Free: 0.292
    Space Group: C 2
    Unit Cell:
      Length [Å] Angles [°]
    a = 168.11 α = 90.00 
    b = 222.13 β = 100.99 
    c = 191.78 γ = 90.00