2JA6

CPD lesion containing RNA Polymerase II elongation complex B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.292 
  • R-Value Observed: 0.292 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

CPD damage recognition by transcribing RNA polymerase II.

Brueckner, F.Hennecke, U.Carell, T.Cramer, P.

(2007) Science 315: 859-862

  • DOI: 10.1126/science.1135400
  • Primary Citation of Related Structures:  
    2JA8, 2JA7, 2JA6, 2JA5

  • PubMed Abstract: 
  • Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II ...

    Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5'-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.


    Organizational Affiliation

    Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT A1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE B1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE C318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE D221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE E215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE F155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE G171Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE H146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 I122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 J70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE K120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE L70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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  • Entity ID: 13
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'N14synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 14
      MoleculeChainsLengthOrganismImage
      5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP)-3'P11synthetic construct
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      Entity ID: 15
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *CP*TP*TP*TTP*TP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'T25synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 4.00 Å
      • R-Value Free: 0.301 
      • R-Value Work: 0.292 
      • R-Value Observed: 0.292 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 223.58α = 90
      b = 393.491β = 90
      c = 283.505γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2007-02-20
        Type: Initial release
      • Version 1.1: 2011-05-08
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 2.0: 2018-03-07
        Changes: Advisory, Atomic model, Database references, Source and taxonomy