RNA Polymerase II Initiation Complex with a 7-nt RNA
DOI:10.2210/pdb3s15/pdb   NDB ID: NA1117
3S15
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transcription/rna/dna
    Structure Weight: 481363.03
    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
    Molecule: RNA (5'-R(*CP*GP*AP*GP*AP*GP*G)-3')
    Polymer: 11 Type: rna Length: 7
    Chains: R
    Details: RNA (7-mer)
    Molecule: DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')
    Polymer: 12 Type: dna Length: 29
    Chains: T
    Details: Template DNA
     
  •   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: Synthetic construct   Taxonomy    
    Polymer: 12
    Scientific Name: Synthetic construct   Taxonomy    
     
  •   Related PDB Entries Hide
    Identifier Details
    3RZD    
    3RZO    
    3S14    
    3S16    
    3S17    
    3S1M    
    3S1N    
    3S1Q    
    3S1R    
    3S2D    
    3S2H    
     
  •   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:NA1117
     
 
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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