3SR2

Crystal Structure of Human XLF-XRCC4 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.97 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.358 
  • R-Value Observed: 0.359 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair.

Hammel, M.Rey, M.Yu, Y.Mani, R.S.Classen, S.Liu, M.Pique, M.E.Fang, S.Mahaney, B.L.Weinfeld, M.Schriemer, D.C.Lees-Miller, S.P.Tainer, J.A.

(2011) J Biol Chem 286: 32638-32650

  • DOI: 10.1074/jbc.M111.272641
  • Primary Citation of Related Structures:  
    3SR2

  • PubMed Abstract: 
  • The XRCC4-like factor (XLF)-XRCC4 complex is essential for nonhomologous end joining, the major repair pathway for DNA double strand breaks in human cells. Yet, how XLF binds XRCC4 and impacts nonhomologous end joining functions has been enigmatic. Here, we report the XLF-XRCC4 complex crystal structure in combination with biophysical and mutational analyses to define the XLF-XRCC4 interactions ...

    The XRCC4-like factor (XLF)-XRCC4 complex is essential for nonhomologous end joining, the major repair pathway for DNA double strand breaks in human cells. Yet, how XLF binds XRCC4 and impacts nonhomologous end joining functions has been enigmatic. Here, we report the XLF-XRCC4 complex crystal structure in combination with biophysical and mutational analyses to define the XLF-XRCC4 interactions. Crystal and solution structures plus mutations characterize alternating XRCC4 and XLF head domain interfaces forming parallel super-helical filaments. XLF Leu-115 ("Leu-lock") inserts into a hydrophobic pocket formed by XRCC4 Met-59, Met-61, Lys-65, Lys-99, Phe-106, and Leu-108 in synergy with pseudo-symmetric β-zipper hydrogen bonds to drive specificity. XLF C terminus and DNA enhance parallel filament formation. Super-helical XLF-XRCC4 filaments form a positively charged channel to bind DNA and align ends for efficient ligation. Collective results reveal how human XLF and XRCC4 interact to bind DNA, suggest consequences of patient mutations, and support a unified molecular mechanism for XLF-XRCC4 stimulation of DNA ligation.


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair protein XRCC4A, B, E, F145Homo 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Non-homologous end-joining factor 1C, D, G, H229Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.97 Å
  • R-Value Free: 0.369 
  • R-Value Work: 0.358 
  • R-Value Observed: 0.359 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.017α = 90
b = 110.017β = 90
c = 763.68γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2011-08-10
    Changes: Database references
  • Version 1.2: 2011-09-28
    Changes: Database references