3W1B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


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:  

  • 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 defi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase 4
A
610Homo sapiensMutation(s): 0 
Gene Names: LIG4
EC: 6.5.1.1
Find proteins for P49917 (Homo sapiens)
Go to Gene View: LIG4
Go to UniProtKB:  P49917
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Artemis-derived peptide
B
11Homo sapiensMutation(s): 0 
Gene Names: DCLRE1C (ARTEMIS, ASCID, SCIDA, SNM1C)
EC: 3.1.-.-
Find proteins for Q96SD1 (Homo sapiens)
Go to Gene View: DCLRE1C
Go to UniProtKB:  Q96SD1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
HG
Query on HG

Download SDF File 
Download CCD File 
A
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.630α = 90.00
b = 105.210β = 90.00
c = 122.040γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
SCALAdata scaling
MOSFLMdata reduction
DNAdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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