5G32

Structure of Rad14 in complex with acetylaminophenyl-guanine containing DNA

• PDB DOI: https://doi.org/10.2210/pdb5G32/pdb
• NAKB: 5G32

• Classification: CELL CYCLE
• Mutation(s): No 


• Deposited: 2016-04-18 Released: 2016-06-01 
• Deposition Author(s): Simon, N., Ebert, C., Schneider, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 

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

• PubMed: 27223336 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.4 kDa 
• Atom Count: 3,071 
• Modelled Residue Count: 285 
• Deposited Residue Count: 320 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.220 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.964	α = 90
b = 52.964	β = 90
c = 130.945	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Simon, N., Ebert, C., Schneider, S.

Revision History  

• 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 2.0: 2017-08-23
  Changes: Atomic model, Data collection
• Version 3.0: 2019-05-15
  Changes: Atomic model, Data collection, Derived calculations, Polymer sequence
• Version 3.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other