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RNA Polymerase II binary complex with DNA
DOI:10.2210/pdb4a3i/pdb   NDB ID: NA2957
4A3I
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transcription
    Structure Weight: 527538.39
    Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
    Polymer: 1 Type: protein Length: 1732
    Chains: A
    EC#: 2.7.7.6   
    Fragment: RESIDUES 1-1732
    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 POLYMERASE II SUBUNIT RPB4
    Polymer: 4 Type: protein Length: 221
    Chains: D
    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 RPABC 1
    Polymer: 5 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 RPABC 2
    Polymer: 6 Type: protein Length: 155
    Chains: F
    Organism: Saccharomyces cerevisiae
    Gene Names: RPO26 RPB6 YPR187W P9677.8
    UniProtKB: Protein Feature View | Search PDB | P20435  
    Molecule: RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
    Polymer: 7 Type: protein Length: 171
    Chains: G
    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 RPABC 3
    Polymer: 8 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: 9 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 RPABC 5
    Polymer: 10 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: 11 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 RPABC 4
    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: 5'-D(*GP*GP*CP*AP*CP*AP*AP*CP*TP*GP*CP*GP*GP*CP*T)-3'
    Polymer: 13 Type: dna Length: 15
    Chains: N
    Organism: synthetic construct
    Molecule: TEMPLATE DNA 27-MER
    Polymer: 14 Type: dna Length: 27
    Chains: T
    Organism: synthetic construct
     
  •   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: Synthetic construct (Saccharomyces cerevisiae)   Taxonomy    
    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: Synthetic construct (synthetic construct)   Taxonomy    
    Polymer: 14
    Scientific Name: Synthetic construct (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 WITHTHE 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 
    2VUM  ALPHA-AMANITIN INHIBITED COMPLETE RNA POLYMERASE II ELONGATION COMPLEX 
    4A3B  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 4NT DNA-RNA HYBRID 
    4A3C  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID 
    4A3D  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 6NT DNA-RNA HYBRID 
    4A3E  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 5NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP 
    4A3F  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 6NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP 
    4A3G  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 2NT DNA-RNA HYBRID 
    4A3J  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 2NT DNA-RNA HYBRID AND SOAKED WITH GMPCPP 
    4A3K  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 7NT DNA-RNA HYBRID 
    4A3L  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 7NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP 
    4A3M  RNA POLYMERASE II INITIAL TRANSCRIBING COMPLEX WITH A 4NT DNA-RNA HYBRID AND SOAKED WITH AMPCPP 
    4A93  RNA POLYMERASE II ELONGATION COMPLEX CONTAINING A CPD LESION 
     
  •   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
    BRU
    Search 
    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: NA2957
     
 
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:   Cheung, A.C.M.,  Sainsbury, S.,  Cramer, P.

    Deposition:   2011-09-30
    Release:   2012-02-08
    Last Modified (REVDAT):   2014-03-19
     
  •   Revision History    Hide
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    2014-03-19
    Other
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    Resolution[Å]:   3.80
    R-Value: 0.159 (obs.)
    R-Free: 0.191
    Space Group: C 2 2 21
    Unit Cell:
      Length [Å] Angles [°]
    a = 221.14 α = 90.00 
    b = 393.18 β = 90.00 
    c = 282.48 γ = 90.00