5G34

Structure of Rad14 in complex with acetylaminoanthracene-C8-guanine containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Bulky Adduct DNA Lesion Recognition by the Nucleotide Excision Repair Protein Rad14.

Schneider, S.Simon, N.Ebert, C.

(2016) Chemistry 22: 10782

  • DOI: https://doi.org/10.1002/chem.201602438
  • Primary Citation of Related Structures:  
    5G32, 5G33, 5G34, 5G35

  • PubMed Abstract: 

    Heterocyclic aromatic amines react with purine bases and result in bulky DNA adducts that cause mutations. Such structurally diverse lesions are substrates for the nucleotide excision repair (NER). It is thought that the NER machinery recognises and verifies distorted DNA conformations, also involving the xeroderma pigmentosum group A and C proteins (XPA, XPC) that act as a scaffold between the DNA substrate and several other NER proteins. Here we present the synthesis of DNA molecules containing the polycyclic, aromatic amine C8-guanine lesions acetylaminophenyl, acetylaminonaphthyl, acetylaminoanthryl, and acetylaminopyrenyl, as well as their crystal structures in complex with the yeast XPA homologue Rad14. This work further substantiates the indirect lesion-detection mechanism employed by the NER system that recognises destabilised and deformable DNA structures.


  • Organizational Affiliation

    Center for Integrated Protein Science Munich CIPSM, Department of Chemistry, Ludwig-Maximilians Universität München, Butenandtstrasse 13, 81377, München, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RAD14
A, B
131Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAD14YMR201CYM8325.02C
UniProt
Find proteins for P28519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28519 
Go to UniProtKB:  P28519
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28519
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*TP*CP*TP*AP*6FKP*TP*CP*AP*TP*CP*AP*CP)-3'
C, E
15synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'
D, F
14synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.218 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.065α = 90
b = 53.065β = 90
c = 130.323γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2016-08-03
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description