5G32

Structure of Rad14 in complex with acetylaminophenyl-guanine containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 2.0 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: 10.1002/chem.201602438
  • Primary Citation of Related Structures:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAD14
A, B
131Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RAD14
Find proteins for P28519 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28519
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*TP*CP*TP*AP*6FKP*TP*CP*AP*TP*CP*AP*CP)-3'C,E15synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*TP*GP*AP*TP*GP*AP*CP*GP*TP*AP*GP*AP*GP)-3'D,F14synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6FK
Query on 6FK
C, E
DNA linkingC18 H21 N6 O8 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 52.964α = 90.00
b = 52.964β = 90.00
c = 130.945γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2016-08-03
    Type: Database references
  • Version 2.0: 2017-08-23
    Type: Atomic model, Data collection