A swapped dimer of the HIV-1 capsid C-terminal domain

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Domain-swapped dimerization of the HIV-1 capsid C-terminal domain

Ivanov, D.Tsodikov, O.V.Kasanov, J.Ellenberger, T.Wagner, G.Collins, T.

(2007) Proc Natl Acad Sci U S A 104: 4353-4358

  • DOI: https://doi.org/10.1073/pnas.0609477104
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Assembly of the HIV and other retroviruses is primarily driven by the oligomerization of the Gag polyprotein, the major viral structural protein capable of forming virus-like particles even in the absence of all other virally encoded components. Several critical determinants of Gag oligomerization are located in the C-terminal domain of the capsid protein (CA-CTD), which encompasses the most conserved segment in the highly variable Gag protein called the major homology region (MHR). The CA-CTD is thought to function as a dimerization module, although the existing model of CA-CTD dimerization does not readily explain why the conserved residues of the MHR are essential for retroviral assembly. Here we describe an x-ray structure of a distinct domain-swapped variant of the HIV-1 CA-CTD dimer stabilized by a single amino acid deletion. In the domain-swapped structure, the MHR-containing segment forms a major part of the dimerization interface, providing a structural mechanism for the enigmatic function of the MHR in HIV assembly. Our observations suggest that swapping of the MHR segments of adjacent Gag molecules may be a critical intermediate in retroviral assembly.

  • Organizational Affiliation

    Department of Pathology, Children's Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA. dmitri.ivanov@hms.harvard.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein p2476Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for Q9IVQ4 (Human immunodeficiency virus 1)
Explore Q9IVQ4 
Go to UniProtKB:  Q9IVQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9IVQ4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.129α = 90
b = 40.129β = 90
c = 105.322γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description