4A93

RNA Polymerase II elongation complex containing a CPD Lesion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Mechanism of Translesion Transcription by RNA Polymerase II and its Role in Cellular Resistance to DNA Damage.

Walmacq, C.Cheung, A.C.Kireeva, M.L.Lubkowska, L.Ye, C.Gotte, D.Strathern, J.N.Carell, T.Cramer, P.Kashlev, M.

(2012) Mol Cell 46: 18

  • DOI: https://doi.org/10.1016/j.molcel.2012.02.006
  • Primary Citation of Related Structures:  
    4A93

  • PubMed Abstract: 

    UV-induced cyclobutane pyrimidine dimers (CPDs) in the template DNA strand stall transcription elongation by RNA polymerase II (Pol II). If the nucleotide excision repair machinery does not promptly remove the CPDs, stalled Pol II creates a roadblock for DNA replication and subsequent rounds of transcription. Here we present evidence that Pol II has an intrinsic capacity for translesion synthesis (TLS) that enables bypass of the CPD with or without repair. Translesion synthesis depends on the trigger loop and bridge helix, the two flexible regions of the Pol II subunit Rpb1 that participate in substrate binding, catalysis, and translocation. Substitutions in Rpb1 that promote lesion bypass in vitro increase UV resistance in vivo, and substitutions that inhibit lesion bypass decrease cell survival after UV irradiation. Thus, translesion transcription becomes essential for cell survival upon accumulation of the unrepaired CPD lesions in genomic DNA.


  • Organizational Affiliation

    NCI Center for Cancer Research, Frederick, MD 21702, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11,732Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB21,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3318Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4221Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RPB7, DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7171Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9122Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 570Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 470Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains LengthOrganismImage
5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP*GP*CP*TP)-3'M [auth N]14Saccharomyces cerevisiae
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Entity ID: 14
MoleculeChains LengthOrganismImage
5'-R(*UP*UP*CP*GP*AP*CP*CP*AP*GP*GP*AP*AP)-3'N [auth P]12Saccharomyces cerevisiae
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Entity ID: 15
MoleculeChains LengthOrganismImage
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*T*TTP*TP*TP*CP*C BRUP*GP*GP*TP*CP*AP*TP*T)-3'O [auth T]25Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 221.637α = 90
b = 391.519β = 90
c = 281.774γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Other
  • Version 1.2: 2012-11-21
    Changes: Other
  • Version 1.3: 2019-01-30
    Changes: Advisory, Data collection, Experimental preparation, Other
  • Version 1.4: 2019-11-20
    Changes: Derived calculations, Other
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description