Experimental Data Snapshot

  • Resolution: 2.53 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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This is version 1.6 of the entry. See complete history


Crystal structure of an active two-domain derivative of Rous sarcoma virus integrase.

Yang, Z.N.Mueser, T.C.Bushman, F.D.Hyde, C.C.

(2000) J Mol Biol 296: 535-548

  • DOI: https://doi.org/10.1006/jmbi.1999.3463
  • Primary Citation of Related Structures:  
    1C0M, 1C1A

  • PubMed Abstract: 

    Integration of retroviral cDNA is a necessary step in viral replication. The virally encoded integrase protein and DNA sequences at the ends of the linear viral cDNA are required for this reaction. Previous studies revealed that truncated forms of Rous sarcoma virus integrase containing two of the three protein domains can carry out integration reactions in vitro. Here, we describe the crystal structure at 2.5 A resolution of a fragment of the integrase of Rous sarcoma virus (residues 49-286) containing both the conserved catalytic domain and a modulatory DNA-binding domain (C domain). The catalytic domains form a symmetric dimer, but the C domains associate asymmetrically with each other and together adopt a canted conformation relative to the catalytic domains. A binding path for the viral cDNA is evident spanning both domain surfaces, allowing modeling of the larger integration complexes that are known to be active in vivo. The modeling suggests that formation of an integrase tetramer (a dimer of dimers) is necessary and sufficient for joining both viral cDNA ends at neighboring sites in the target DNA. The observed asymmetric arrangement of C domains suggests that they could form a rotationally symmetric tetramer that may be important for bridging integrase complexes at each cDNA end.

  • Organizational Affiliation

    Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
238Rous sarcoma virusMutation(s): 1 
Find proteins for P03354 (Rous sarcoma virus subgroup C (strain Prague))
Explore P03354 
Go to UniProtKB:  P03354
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03354
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.53 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.752α = 67.47
b = 66.369β = 78.61
c = 76.67γ = 90.18
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-14
    Changes: Database references
  • Version 1.4: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection
  • Version 1.6: 2024-02-07
    Changes: Data collection, Database references