3VNN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.903 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 10.1016/j.str.2012.04.012

  • 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 s ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase 4
A
139Homo sapiensGene Names: LIG4
EC: 6.5.1.1
Find proteins for P49917 (Homo sapiens)
Go to Gene View: LIG4
Go to UniProtKB:  P49917
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.903 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.273 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 39.086α = 90.00
b = 39.086β = 90.00
c = 197.393γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SOLVEphasing
PHENIXrefinement
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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