2X78

Human foamy virus integrase - catalytic core.

• PDB DOI: https://doi.org/10.2210/pdb2X78/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human spumaretrovirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-24 Released: 2010-08-11 
• Deposition Author(s): Rety, S., Delelis, O., Rezabkova, L., Dubanchet, B., Legrand, P., Silhan, J., Lewit-Bentley, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Structural Studies of the Catalytic Core of the Primate Foamy Virus (Pfv-1) Integrase

Rety, S., Rezabkova, L., Dubanchet, B., Silhan, J., Legrand, P., Lewit-Bentley, A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 881

• PubMed: 20693659 
• DOI: https://doi.org/10.1107/S1744309110022852
• Primary Citation of Related Structures:  
  2X6N, 2X6S, 2X74, 2X78


• PubMed Abstract: 
  

  Retroviral integrases are vital enzymes in the viral life cycle and thus are important targets for antiretroviral drugs. The structure of the catalytic core domain of the integrase from human foamy virus, which is related to HIV-1, has been solved. The structure of the protein is presented in two different crystal forms, each containing several molecules in the asymmetric unit, with and without the essential manganese or magnesium ion, and the structures are compared in detail. This allows regions of high structural variability to be pinpointed, as well as the effect of divalent cations on the conformation of the catalytic site.

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Organizational Affiliation: 

Laboratoire de Biologie et Pharmacologie Appliquée, CNRS UMR8113, Ecole Normale Supérieure de Cachan, 61 Avenue du Président Wilson, 94235 Cachan, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 67.57 kDa 
• Atom Count: 4,626 
• Modelled Residue Count: 530 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
INTEGRASE	A, B, C	200	Human spumaretrovirus	Mutation(s): 0
UniProt
Find proteins for P14350 (Human spumaretrovirus) Explore P14350  Go to UniProtKB:  P14350

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.272 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.8	α = 90
b = 98.04	β = 90
c = 240.32	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Rety, S., Delelis, O., Rezabkova, L., Dubanchet, B., Legrand, P., Silhan, J., Lewit-Bentley, A.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references, Other, Refinement description, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description