Crystal structure of catalytic core domain of BIV integrase in crystal form II

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

Starting Model: experimental
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Crystal structures of catalytic core domain of BIV integrase: implications for the interaction between integrase and target DNA

Yao, X.Fang, S.Qiao, W.Geng, Y.Shen, Y.

(2010) Protein Cell 1: 363-370

  • DOI: https://doi.org/10.1007/s13238-010-0047-5
  • Primary Citation of Related Structures:  
    3KKR, 3KKS

  • PubMed Abstract: 

    Integrase plays a critical role in the recombination of viral DNA into the host genome. Therefore, over the past decade, it has been a hot target of drug design in the fight against type 1 human immunodeficiency virus (HIV-1). Bovine immunodeficiency virus (BIV) integrase has the same function as HIV-1 integrase. We have determined crystal structures of the BIV integrase catalytic core domain (CCD) in two different crystal forms at a resolution of 2.45 Å and 2.2 Å, respectively. In crystal form I, BIV integrase CCD forms a back-to-back dimer, in which the two active sites are on opposite sides. This has also been seen in many of the CCD structures of HIV-1 integrase that were determined previously. However, in crystal form II, BIV integrase CCD forms a novel face-to-face dimer in which the two active sites are close to each other. Strikingly, the distance separating the two active sites is approximately 20 Å, a distance that perfectly matches a 5-base pair interval. Based on these data, we propose a model for the interaction of integrase with its target DNA, which is also supported by many published biochemical data. Our results provide important clues for designing new inhibitors against HIV-1.

  • Organizational Affiliation

    Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
152Bovine immunodeficiency virus R29Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P19560 (Bovine immunodeficiency virus (strain R29))
Explore P19560 
Go to UniProtKB:  P19560
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19560
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.054α = 90
b = 88.054β = 90
c = 81.775γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2010-09-22 
  • Deposition Author(s): Shen, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description