Biological Assembly 1  

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

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: 44.67 kDa 
• Atom Count: 2972 
• Modelled Residue Count: 345 
• Deposited Residue Count: 389 
• Unique protein chains: 2

3LQC

X-ray crystal structure of oxidized XRCC1 bound to DNA pol beta Palm thumb domain

• PDB DOI: 10.2210/pdb3LQC/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-09 Released: 2010-04-28 
• Deposition Author(s): Cuneo, M.J., Krahn, J.M., London, R.E.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.250 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Literature

Oxidation state of the XRCC1 N-terminal domain regulates DNA polymerase beta binding affinity.

Cuneo, M.J., London, R.E.

(2010) Proc Natl Acad Sci U S A 107: 6805-6810

• PubMed: 20351257 
• DOI: 10.1073/pnas.0914077107
• Primary Citation of Related Structures:  
  3K75, 3K77, 3LQC


• PubMed Abstract: 
  

Formation of a complex between the XRCC1 N-terminal domain (NTD) and DNA polymerase beta (Pol beta) is central to base excision repair of damaged DNA. Two crystal forms of XRCC1-NTD complexed with Pol beta have been solved, revealing that the XRCC1-NTD is able to adopt a redox-dependent alternate fold, characterized by a disulfide bond, and substantial variations of secondary structure, folding topology, and electrostatic surface. Although most of these structural changes occur distal to the interface, the oxidized XRCC1-NTD forms additional interactions with Pol beta, enhancing affinity by an order of magnitude. Transient disulfide bond formation is increasingly recognized as an important molecular regulatory mechanism. The results presented here suggest a paradigm in DNA repair in which the redox state of a scaffolding protein plays an active role in organizing the repair complex.

---

Organizational Affiliation: 

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein XRCC1	A	189	Homo sapiens	Mutation(s): 0  Gene Names: XRCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P18887 (Homo sapiens) Explore P18887  Go to UniProtKB:  P18887
PHAROS:  P18887

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	B	200	Rattus norvegicus	Mutation(s): 0  Gene Names: Polb EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt
Find proteins for P06766 (Rattus norvegicus) Explore P06766  Go to UniProtKB:  P06766

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO3	D [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.250 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.24	α = 90
b = 75.24	β = 90
c = 126.16	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-09 
• Released Date: 2010-04-28 
Deposition Author(s): Cuneo, M.J., Krahn, J.M., London, R.E.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance