Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.277 

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Structural insights into the role of domain flexibility in human DNA ligase IV

Ochi, T.Wu, Q.Chirgadze, D.Y.Grossmann, J.G.Bolanos-Garcia, V.M.Blundell, T.L.

(2012) Structure 20: 1212-1222

  • DOI: https://doi.org/10.1016/j.str.2012.04.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Knowledge of the architecture of DNA ligase IV (LigIV) and interactions with XRCC4 and XLF-Cernunnos is necessary for understanding its role in the ligation of double-strand breaks during nonhomologous end joining. Here we report the structure of a subdomain of the nucleotidyltrasferase domain of human LigIV and provide insights into the residues associated with LIG4 syndrome. We use this structural information together with the known structures of the BRCT/XRCC4 complex and those of LigIV orthologs to interpret small-angle X-ray scattering of LigIV in complex with XRCC4 and size exclusion chromatography of LigIV, XRCC4, and XLF-Cernunnos. Our results suggest that the flexibility of the catalytic region is limited in a manner that affects the formation of the LigIV/XRCC4/XLF-Cernunnos complex.

  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. to237@cam.ac.uk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA ligase 4139Homo sapiensMutation(s): 0 
Gene Names: LIG4
UniProt & NIH Common Fund Data Resources
Find proteins for P49917 (Homo sapiens)
Explore P49917 
Go to UniProtKB:  P49917
GTEx:  ENSG00000174405 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49917
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.277 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.086α = 90
b = 39.086β = 90
c = 197.393γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references