6ERG

Complex of XLF and heterodimer Ku bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.

Nemoz, C.Ropars, V.Frit, P.Gontier, A.Drevet, P.Yu, J.Guerois, R.Pitois, A.Comte, A.Delteil, C.Barboule, N.Legrand, P.Baconnais, S.Yin, Y.Tadi, S.Barbet-Massin, E.Berger, I.Le Cam, E.Modesti, M.Rothenberg, E.Calsou, P.Charbonnier, J.B.

(2018) Nat. Struct. Mol. Biol. 25: 971-980

  • DOI: 10.1038/s41594-018-0133-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined cryst ...

    The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBM motifs bind remote sites of the Ku80 α/β domain. The X-KBM occupies an internal pocket formed by an unprecedented large outward rotation of the Ku80 α/β domain. We observe independent recruitment of the APLF-interacting protein XRCC4 and of XLF to laser-irradiated sites via binding of A- and X-KBMs, respectively, to Ku80. Finally, we show that mutation of the X-KBM and A-KBM binding sites in Ku80 compromises both the efficiency and accuracy of end joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchor points to build the intricate interaction network required for NHEJ.


    Organizational Affiliation

    Signalisations, Noyaux et Innovations en Cancérologie, UMR 8126, CNRS, Université Paris-Sud, Gustave Roussy, Université Paris-Saclay, Villejuif, France.,Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France. jb.charbonnier@cea.fr.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France. calsou@ipbs.fr.,Cancer Research Center of Marseille, CNRS UMR 7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France.,Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.,Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France.,Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,New York University School of Medicine, Perlmutter Cancer Center, New York, USA.,Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France.,Dynamic Biosensors GmbH, Martinsried, Germany.,BrisSynBio Centre, School of Biochemistry, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK.,Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France. calsou@ipbs.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
X-ray repair cross-complementing protein 6
A, D
544Homo sapiensMutation(s): 0 
Gene Names: XRCC6 (G22P1)
EC: 3.6.4.-, 4.2.99.-
Find proteins for P12956 (Homo sapiens)
Go to Gene View: XRCC6
Go to UniProtKB:  P12956
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
X-ray repair cross-complementing protein 5
B, E
572Homo sapiensMutation(s): 0 
Gene Names: XRCC5 (G22P2)
EC: 3.6.4.-
Find proteins for P13010 (Homo sapiens)
Go to Gene View: XRCC5
Go to UniProtKB:  P13010
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Non-homologous end-joining factor 1
C, F
13Homo sapiensMutation(s): 0 
Gene Names: NHEJ1 (XLF)
Find proteins for Q9H9Q4 (Homo sapiens)
Go to Gene View: NHEJ1
Go to UniProtKB:  Q9H9Q4
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (21-MER)H,K21synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA (34-MER)M,R34synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 111.710α = 90.00
b = 114.260β = 93.14
c = 127.170γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
INCAFrancePLBIO 2012-280
French National Research AgencyFranceANR-12-SVSE8-012

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Data collection, Source and taxonomy