3Q4F

Crystal structure of xrcc4/xlf-cernunnos complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of filaments formed by human Xrcc4-Cernunnos/XLF complex involved in nonhomologous DNA end-joining.

Ropars, V.Drevet, P.Legrand, P.Baconnais, S.Amram, J.Faure, G.Marquez, J.A.Pietrement, O.Guerois, R.Callebaut, I.Le Cam, E.Revy, P.de Villartay, J.P.Charbonnier, J.B.

(2011) Proc Natl Acad Sci U S A 108: 12663-12668

  • DOI: 10.1073/pnas.1100758108
  • Primary Citation of Related Structures:  
    3Q4F

  • PubMed Abstract: 
  • Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4) ...

    Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X4(1-157)-Cernunnos(1-224) complex at 5.5-Å resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X4(1-157) and Cernunnos(1-224) homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4-Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4-Cernunnos interface. We identified four X4 residues (Glu(55), Asp(58), Met(61), and Phe(106)) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step.


    Organizational Affiliation

    Laboratory of Structural Biology and Radiobiology, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut de Biologie et de Technologies de Saclay, 91191 Gif-s-Yvette, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1E [auth A], F [auth B], A [auth E], B [auth F]230Homo sapiensMutation(s): 0 
Gene Names: NHEJ1XLF
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q4 (Homo sapiens)
Explore Q9H9Q4 
Go to UniProtKB:  Q9H9Q4
PHAROS:  Q9H9Q4
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein XRCC4C, D, G, H186Homo sapiensMutation(s): 0 
Gene Names: XRCC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13426 (Homo sapiens)
Explore Q13426 
Go to UniProtKB:  Q13426
PHAROS:  Q13426
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.86α = 90
b = 103.86β = 90
c = 855.22γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-03
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references