Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

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This is version 1.3 of the entry. See complete history


Structures of the HIV-1 capsid protein dimerization domain at 2.6 A resolution.

Worthylake, D.K.Wang, H.Yoo, S.Sundquist, W.I.Hill, C.P.

(1999) Acta Crystallogr D Biol Crystallogr 55: 85-92

  • DOI: https://doi.org/10.1107/S0907444998007689
  • Primary Citation of Related Structures:  
    1A43, 1BAJ

  • PubMed Abstract: 

    The human immunodeficiency virus type I (HIV-1) capsid protein is initially synthesized as the central domain of the Gag polyprotein, and is subsequently proteolytically processed into a discrete 231-amino-acid protein that forms the distinctive conical core of the mature virus. The crystal structures of two proteins that span the C-terminal domain of the capsid are reported here: one encompassing residues 146-231 (CA146-231) and the other extending to include the 14-residue p2 domain of Gag (CA146-p2). The isomorphous CA146-231 and CA146-p2 structures were determined by molecular replacement and have been refined at 2.6 A resolution to R factors of 22.3 and 20.7% (Rfree = 28.1 and 27.5%), respectively. The ordered domains comprise residues 148-219 for CA146-231 and 148-218 for CA146-p2, and their refined structures are essentially identical. The proteins are composed of a 310 helix followed by an extended strand and four alpha-helices. A crystallographic twofold generates a dimer that is stabilized by parallel packing of an alpha-helix 2 across the dimer interface and by packing of the 310 helix into a groove created by alpha-helices 2 and 3 of the partner molecule. CA146-231 and CA146-p2 dimerize with the full affinity of the intact capsid protein, and their structures therefore reveal the essential dimer interface of the HIV-1 capsid.

  • Organizational Affiliation

    Biochemistry Department, University of Utah Medical School, 50 North Medical Drive, Salt Lake City, Utah 84132, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GAG POLYPROTEIN101Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: GAG
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.33α = 90
b = 61.33β = 90
c = 59.57γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Refinement description