Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 53.26 kDa 
• Atom Count: 3736 
• Residue Count: 430 
• Unique protein chains: 2

1IK9

CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX

• DOI: 10.2210/pdb1IK9/pdb

• Classification: GENE REGULATION/LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-05-03 Released: 2001-11-21 
• Deposition Author(s): Sibanda, B.L., Critchlow, S.E., Begun, J., Pei, X.Y., Jackson, S.P., Blundell, T.L., Pellegrini, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.266 
• R-Value Work: 0.228 

Literature

Crystal structure of an Xrcc4-DNA ligase IV complex.

Sibanda, B.L., Critchlow, S.E., Begun, J., Pei, X.Y., Jackson, S.P., Blundell, T.L., Pellegrini, L.

(2001) Nat Struct Biol 8: 1015-1019

• PubMed: 11702069 
• DOI: 10.1038/nsb725
• Primary Citation of Related Structures:  
  1IK9


• PubMed Abstract: 
  

A complex of two proteins, Xrcc4 and DNA ligase IV, plays a fundamental role in DNA non-homologous end joining (NHEJ), a cellular function required for double-strand break repair and V(D)J recombination. Here we report the crystal structure of human Xrcc4 bound to a polypeptide that corresponds to the DNA ligase IV sequence linking its two BRCA1 C-terminal (BRCT) domains. In the complex, a single ligase chain binds asymmetrically to an Xrcc4 dimer. The helical tails of Xrcc4 undergo a substantial conformational change relative to the uncomplexed protein, forming a coiled coil that unwinds upon ligase binding, leading to a flat interaction surface. A buried network of charged hydrogen bonds surrounded by extensive hydrophobic contacts explains the observed tightness of the interaction. The strong conservation of residues at the interface between the two proteins provides evidence that the observed mode of interaction has been maintained in NHEJ throughout evolution.

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Organizational Affiliation: 

Department of Biochemistry, Cambridge University, Tennis Court Road, Cambridge CB2 1GA, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA REPAIR PROTEIN XRCC4	A, B	213	Homo sapiens	Mutation(s): 4  Gene Names: XRCC4
Find proteins for Q13426 (Homo sapiens) Explore Q13426  Go to UniProtKB:  Q13426
NIH Common Fund Data Resources
PHAROS  Q13426 GTEx  ENSG00000152422

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA LIGASE IV	C	37	Homo sapiens	Mutation(s): 0  Gene Names: LIG4 EC: 6.5.1.1
Find proteins for P49917 (Homo sapiens) Explore P49917  Go to UniProtKB:  P49917
NIH Common Fund Data Resources
PHAROS  P49917 GTEx  ENSG00000174405

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.266 
• R-Value Work: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.062	α = 90
b = 79.628	β = 90
c = 242.142	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-05-03 
• Released Date: 2001-11-21 
Deposition Author(s): Sibanda, B.L., Critchlow, S.E., Begun, J., Pei, X.Y., Jackson, S.P., Blundell, T.L., Pellegrini, L.

Revision History 

• Version 1.0: 2001-11-21
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance