2QSG

Crystal structure of Rad4-Rad23 bound to a UV-damaged DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

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This is version 2.0 of the entry. See complete history


Literature

Recognition of DNA damage by the Rad4 nucleotide excision repair protein

Min, J.-H.Pavletich, N.P.

(2007) Nature 449: 570-575

  • DOI: https://doi.org/10.1038/nature06155
  • Primary Citation of Related Structures:  
    2QSF, 2QSG, 2QSH

  • PubMed Abstract: 

    Mutations in the nucleotide excision repair (NER) pathway can cause the xeroderma pigmentosum skin cancer predisposition syndrome. NER lesions are limited to one DNA strand, but otherwise they are chemically and structurally diverse, being caused by a wide variety of genotoxic chemicals and ultraviolet radiation. The xeroderma pigmentosum C (XPC) protein has a central role in initiating global-genome NER by recognizing the lesion and recruiting downstream factors. Here we present the crystal structure of the yeast XPC orthologue Rad4 bound to DNA containing a cyclobutane pyrimidine dimer (CPD) lesion. The structure shows that Rad4 inserts a beta-hairpin through the DNA duplex, causing the two damaged base pairs to flip out of the double helix. The expelled nucleotides of the undamaged strand are recognized by Rad4, whereas the two CPD-linked nucleotides become disordered. These findings indicate that the lesions recognized by Rad4/XPC thermodynamically destabilize the Watson-Crick double helix in a manner that facilitates the flipping-out of two base pairs.


  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair protein RAD4C [auth A]533Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD4
UniProt
Find proteins for P14736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P14736 
Go to UniProtKB:  P14736
Entity Groups  
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UniProt GroupP14736
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UV excision repair protein RAD23D [auth X]171Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD23
UniProt
Find proteins for P32628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32628 
Go to UniProtKB:  P32628
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32628
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
native strand of the CPD-mismatch DNAA [auth W]24N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
damaged strand of the CPD-mismatch DNAB [auth Y]24N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.644α = 90
b = 79.644β = 90
c = 403.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2024-02-21
    Changes: Data collection, Database references, Polymer sequence