POP-OUT | CLOSE
 
Cisplatin lesion containing RNA polymerase II elongation complex
DOI:10.2210/pdb2r7z/pdb   NDB ID: PH0044
2R7Z
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transcription/dna RNA Hybrid
    Structure Weight: 525501.92
    Molecule: 5'-D(*TP*AP*CP*TP*TP*GUP*CP*CP*CP*TP*CP*CP*TP*CP*AP*T)-3'
    Polymer: 1 Type: dna Length: 17
    Chains: T
    Molecule: 5'-D(*CP*AP*AP*GP*TP*AP*G)-3'
    Polymer: 2 Type: dna Length: 7
    Chains: N
    Molecule: 5'-R(*UP*UP*UP*GP*AP*GP*GP*AP*GP*G)-3'
    Polymer: 3 Type: rna Length: 10
    Chains: P
    Molecule: DNA-directed RNA polymerase II subunit RPB1
    Polymer: 4 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: 5 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: 6 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: 7 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: 8 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: 9 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 subunit RPB7
    Polymer: 10 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: 11 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: 12 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: 13 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: 14 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: 15 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  
     
  •   Structure Validation Hide

    Download full validation report    

     

  • MolProbity Ramachandran Plot
     

  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 2
    Scientific Name: Synthetic construct   Taxonomy    
    Polymer: 3
    Scientific Name: Synthetic construct   Taxonomy    
    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: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 12
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 13
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 14
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
    Polymer: 15
    Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Baker's yeast  
     
  •   Ligand Chemical Component Hide
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
  • Nucleic Acid Database Hide
    View the NDB ID associated with this structure: PH0044
     
 
Data in orange boxes are gathered from external resources (when available).
 
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
Downloadable viewers:
 
 
 
  •   MyPDB Personal Annotations Hide
     
  •   Deposition Summary Hide
    Authors:   Damsma, G.E.,  Alt, A.,  Brueckner, F.,  Carell, T.,  Cramer, P.

    Deposition:   2007-09-10
    Release:   2007-11-20
    Last Modified (REVDAT):   2012-09-05
     
  •   Revision History    Hide
    Mouse over text for details
    2012-09-05
    Biological assembly
    2011-07-13
    Version format compliance
    2011-07-13
    Non-polymer description
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   3.80
    R-Value: 0.215 (work)
    R-Free: 0.240
    Space Group: C 2 2 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 222.06 α = 90.00 
    b = 393.12 β = 90.00 
    c = 283.73 γ = 90.00