Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.92 kDa 
• Atom Count: 5073 
• Modelled Residue Count: 590 
• Deposited Residue Count: 704 
• Unique protein chains: 2

2QSF

Crystal structure of the Rad4-Rad23 complex

• PDB DOI: 10.2210/pdb2QSF/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2007-07-31 Released: 2007-10-02 
• Deposition Author(s): Min, J.-H., Pavletich, N.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.245 
• R-Value Work: 0.226 

Literature

Recognition of DNA damage by the Rad4 nucleotide excision repair protein

Min, J.-H., Pavletich, N.P.

(2007) Nature 449: 570-575

• PubMed: 17882165 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD4	A	533	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: RAD4
UniProt
Find proteins for P14736 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14736  Go to UniProtKB:  P14736

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UV excision repair protein RAD23	B [auth X]	171	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: RAD23
UniProt
Find proteins for P32628 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32628  Go to UniProtKB:  P32628

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.245 
• R-Value Work: 0.226 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.167	α = 90
b = 115.711	β = 105.7
c = 113.947	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-31 
• Released Date: 2007-10-02 
Deposition Author(s): Min, J.-H., Pavletich, N.P.

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance