1Z56

Co-Crystal Structure of Lif1p-Lig4p


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free: 0.467 
  • R-Value Work: 0.400 
  • R-Value Observed: 0.403 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode.

Dore, A.S.Furnham, N.Davies, O.R.Sibanda, B.L.Chirgadze, D.Y.Jackson, S.P.Pellegrini, L.Blundell, T.L.

(2006) DNA Repair (Amst) 5: 362-368

  • DOI: 10.1016/j.dnarep.2005.11.004
  • Primary Citation of Related Structures:  
    1Z56

  • PubMed Abstract: 
  • DNA ligase IV catalyses the final ligation step in the non-homologous end-joining (NHEJ) DNA repair pathway and requires interaction of the ligase with the Xrcc4 'genome-guardian', an essential NHEJ factor. Here we report the 3.9 A crystal structure of the Saccharomyces cerevisiae Xrcc4 ortholog ligase interacting factor 1 (Lif1p) complexed with the C-terminal BRCT domains of DNA ligase IV (Lig4p) ...

    DNA ligase IV catalyses the final ligation step in the non-homologous end-joining (NHEJ) DNA repair pathway and requires interaction of the ligase with the Xrcc4 'genome-guardian', an essential NHEJ factor. Here we report the 3.9 A crystal structure of the Saccharomyces cerevisiae Xrcc4 ortholog ligase interacting factor 1 (Lif1p) complexed with the C-terminal BRCT domains of DNA ligase IV (Lig4p). The structure reveals a novel mode of protein recognition by a tandem BRCT repeat, and in addition provides a molecular basis for a human LIG4 syndrome clinical condition.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. Andrew.Dore@icr.ac.uk



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1A, B246Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
Find proteins for P53150 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P53150
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase IVC264Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DNL4LIG4
EC: 6.5.1.1
Find proteins for Q08387 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q08387
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1D8Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1E, H7Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1F45Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1G37Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1I30Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1J20Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ligase interacting factor 1K13Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LIF1
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free: 0.467 
  • R-Value Work: 0.400 
  • R-Value Observed: 0.403 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.617α = 90
b = 247.617β = 90
c = 98.416γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description