1IK9

CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX

Experimental Data Snapshot

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

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This is version 1.3 of the entry. See complete history. 


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

  • 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 ...

    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.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA REPAIR PROTEIN XRCC4A, B213Homo sapiensMutation(s): 4 
Gene Names: XRCC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13426 (Homo sapiens)
Explore Q13426 
Go to UniProtKB:  Q13426
PHAROS:  Q13426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13426
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA LIGASE IVC37Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49917 (Homo sapiens)
Explore P49917 
Go to UniProtKB:  P49917
PHAROS:  P49917
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49917
Protein Feature View
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  • Reference Sequence
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 = 45.062α = 90
b = 79.628β = 90
c = 242.142γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2021-10-27
    Changes: Database references