Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 142396.50 
• Atom Count: 8975 
• Residue Count: 1220 
• Unique protein chains: 1

3W5O

Crystal Structure of Human DNA ligase IV

• DOI: 10.2210/pdb3W5O/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-02-02 Released: 2013-04-03 
• Deposition Author(s): Gu, X., Ochi, T., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.245 
• R-Value Work: 0.194 

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

• PubMed: 23523427 
• DOI: 10.1016/j.str.2013.02.014
• Primary Citation of Related Structures:  
  3W1G, 3W1B


• 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. 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.

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Organizational Affiliation: 

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA ligase 4	A, B	610	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	A, B	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.245 
• R-Value Work: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 68.290	α = 90.00
b = 104.360	β = 94.08
c = 120.040	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
MxCuBE	data collection
XDS	data reduction
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-02 
• Released Date: 2013-04-03 
• Deposition Author(s): Gu, X., Ochi, T., Blundell, T.L.

Revision History 

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