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 

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 5: 362-368

  • DOI: 10.1016/j.dnarep.2005.11.004

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
A, B
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: LIF1
Find proteins for P53150 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53150
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA ligase IV
C
264Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: DNL4 (LIG4)
EC: 6.5.1.1
Find proteins for Q08387 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08387
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
D
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
E, H
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
F
45N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
G
37N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
I
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
J
20N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ligase interacting factor 1
K
13N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
D, E, F, G, H, I, J, K
L-PEPTIDE LINKINGC4 H9 N O2

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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 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 247.617α = 90.00
b = 247.617β = 90.00
c = 98.416γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALEPACKdata scaling
REFMACrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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