3W1B

Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 

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This is version 1.1 of the entry. See complete history


Literature

Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break repair

Ochi, T.Gu, X.Blundell, T.L.

(2013) Structure 21: 672-679

  • DOI: 10.1016/j.str.2013.02.014
  • Primary Citation of Related Structures:  
    3W1G, 3W1B, 3W5O

  • PubMed Abstract: 
  • Nonhomologous end joining (NHEJ) is central to the repair of double-stranded DNA breaks throughout the cell cycle and plays roles in the development of the immune system. Although three-dimensional structures of most components of NHEJ have been defined, those of the catalytic region of DNA ligase IV (LigIV), a specialized DNA ligase known to work in NHEJ, and of Artemis have remained unresolved ...

    Nonhomologous end joining (NHEJ) is central to the repair of double-stranded DNA breaks throughout the cell cycle and plays roles in the development of the immune system. Although three-dimensional structures of most components of NHEJ have been defined, those of the catalytic region of DNA ligase IV (LigIV), a specialized DNA ligase known to work in NHEJ, and of Artemis have remained unresolved. Here, we report the crystal structure at 2.4 Å resolution of the catalytic region of LigIV (residues 1-609) in complex with an Artemis peptide. We describe interactions of the DNA-binding domain of LigIV with the continuous epitope of Artemis, which, together, form a three-helix bundle. A kink in the first helix of LigIV introduced by a conserved VPF motif gives rise to a hydrophobic pocket, which accommodates a conserved tryptophan from Artemis. We provide structural insights into features of LigIV among human DNA ligases.


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. to237@cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase 4 A610Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
Find proteins for P49917 (Homo sapiens)
Explore P49917 
Go to UniProtKB:  P49917
NIH Common Fund Data Resources
PHAROS:  P49917
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Artemis-derived peptide B11Homo sapiensMutation(s): 0 
Gene Names: DCLRE1CARTEMISASCIDSCIDASNM1C
EC: 3.1
Find proteins for Q96SD1 (Homo sapiens)
Explore Q96SD1 
Go to UniProtKB:  Q96SD1
NIH Common Fund Data Resources
PHAROS:  Q96SD1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.179 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.63α = 90
b = 105.21β = 90
c = 122.04γ = 90
Software Package:
Software NamePurpose
DNAdata collection
SOLVEphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-08-14
    Changes: Database references