3VNN

Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV

• PDB DOI: https://doi.org/10.2210/pdb3VNN/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-17 Released: 2012-06-20 
• Deposition Author(s): Ochi, T., Wu, Q., Chirgadze, D.Y., Grossmann, J.G., Bolanos-Garcia, V.M., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.305 
• R-Value Work: 0.273 
• R-Value Observed: 0.277 

Literature

Structural insights into the role of domain flexibility in human DNA ligase IV

Ochi, T., Wu, Q., Chirgadze, D.Y., Grossmann, J.G., Bolanos-Garcia, V.M., Blundell, T.L.

(2012) Structure 20: 1212-1222

• PubMed: 22658747 
• DOI: https://doi.org/10.1016/j.str.2012.04.012
• Primary Citation of Related Structures:  
  3VNN


• PubMed Abstract: 
  

  Knowledge of the architecture of DNA ligase IV (LigIV) and interactions with XRCC4 and XLF-Cernunnos is necessary for understanding its role in the ligation of double-strand breaks during nonhomologous end joining. Here we report the structure of a subdomain of the nucleotidyltrasferase domain of human LigIV and provide insights into the residues associated with LIG4 syndrome. We use this structural information together with the known structures of the BRCT/XRCC4 complex and those of LigIV orthologs to interpret small-angle X-ray scattering of LigIV in complex with XRCC4 and size exclusion chromatography of LigIV, XRCC4, and XLF-Cernunnos. Our results suggest that the flexibility of the catalytic region is limited in a manner that affects the formation of the LigIV/XRCC4/XLF-Cernunnos complex.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.2 kDa 
• Atom Count: 952 
• Modelled Residue Count: 124 
• Deposited Residue Count: 139 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase 4	A	139	Homo sapiens	Mutation(s): 0  Gene Names: LIG4 EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49917 (Homo sapiens) Explore P49917  Go to UniProtKB:  P49917
PHAROS:  P49917 GTEx:  ENSG00000174405

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.305 
• R-Value Work: 0.273 
• R-Value Observed: 0.277 
• Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.086	α = 90
b = 39.086	β = 90
c = 197.393	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
SOLVE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-20 
Deposition Author(s): Ochi, T., Wu, Q., Chirgadze, D.Y., Grossmann, J.G., Bolanos-Garcia, V.M., Blundell, T.L.

Revision History  

• Version 1.0: 2012-06-20
  Type: Initial release
  
• Version 1.1: 2013-07-24
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references