Yeast RNAP II containing poly(A)-signal sequence in the active site
DOI:10.2210/pdb3h3v/pdb   NDB ID: PH0061
3H3V
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase/dna/rna
    Structure Weight: 531999.18
    Molecule: DNA-directed RNA polymerase II subunit RPB1
    Polymer: 1 Type: protein Length: 1733
    Chains: B
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Molecule: DNA-directed RNA polymerase II subunit RPB2
    Polymer: 2 Type: protein Length: 1224
    Chains: C
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Molecule: DNA-directed RNA polymerase II subunit RPB3
    Polymer: 3 Type: protein Length: 318
    Chains: D
    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: E
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Molecule: DNA-directed RNA polymerases I, II, and III subunit RPABC1
    Polymer: 5 Type: protein Length: 215
    Chains: F
    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: G
    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 subunit RPB7
    Polymer: 7 Type: protein Length: 171
    Chains: H
    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: I
    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: J
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Molecule: DNA-directed RNA polymerases I, II, and III subunit RPABC5
    Polymer: 10 Type: protein Length: 70
    Chains: K
    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: L
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Molecule: DNA-directed RNA polymerases I, II, and III subunit RPABC4
    Polymer: 12 Type: protein Length: 70
    Chains: M
    EC#: 2.7.7.6   
    Organism: Saccharomyces cerevisiae
    Gene Names: RPC10 RPB12 YHR143W-A YHR143BW
    UniProtKB: Protein Feature View | Search PDB | P40422  
    Molecule: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*GP*CP*TP*GP*CP*TP*TP*TP*AP*TP*TP*GP*CP*AP*TP*T)-3'
    Polymer: 13 Type: dna Length: 14
    Chains: N
    Molecule: 5'-D(*CP*AP*GP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3'
    Polymer: 14 Type: rna Length: 16
    Chains: P
    Molecule: 5'-R(*UP*GP*CP*AP*UP*UP*UP*CP*GP*CP*AP*AP*UP*AP*AP*A)-3'
    Polymer: 15 Type: dna Length: 26
    Chains: T
     
  •   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: Yeast  
    Polymer: 2
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 3
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 4
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 5
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 6
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 7
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 8
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 9
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 10
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 11
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 12
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Yeast  
    Polymer: 13
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 14
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 15
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   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
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure:PH0061
     
 
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:   Dengl, S.,  Cramer, P.

    Deposition:   2009-04-17
    Release:   2009-06-16
    Last Modified (REVDAT):   2013-11-06
     
  •   Revision History    Hide
    Mouse over text for details
    2013-11-06
    Data collection
    2011-07-13
    Version format compliance
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   4.00
    R-Value: 0.205 (obs.)
    R-Free: 0.241
    Space Group: C 2 2 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 222.47 α = 90.00 
    b = 391.62 β = 90.00 
    c = 284.12 γ = 90.00