X-ray Structure of Hexameric HIV-1 CA

Experimental Data Snapshot

  • Resolution: 7.00 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.286 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


X-ray structures of the hexameric building block of the HIV capsid.

Pornillos, O.Ganser-Pornillos, B.K.Kelly, B.N.Hua, Y.Whitby, F.G.Stout, C.D.Sundquist, W.I.Hill, C.P.Yeager, M.

(2009) Cell 137: 1282-1292

  • DOI: https://doi.org/10.1016/j.cell.2009.04.063
  • Primary Citation of Related Structures:  
    3GV2, 3H47, 3H4E

  • PubMed Abstract: 

    The mature capsids of HIV and other retroviruses organize and package the viral genome and its associated enzymes for delivery into host cells. The HIV capsid is a fullerene cone: a variably curved, closed shell composed of approximately 250 hexamers and exactly 12 pentamers of the viral CA protein. We devised methods for isolating soluble, assembly-competent CA hexamers and derived four crystallographically independent models that define the structure of this capsid assembly unit at atomic resolution. A ring of six CA N-terminal domains form an apparently rigid core, surrounded by an outer ring of C-terminal domains. Mobility of the outer ring appears to be an underlying mechanism for generating the variably curved lattice in authentic capsids. Hexamer-stabilizing interfaces are highly hydrated, and this property may be key to the formation of quasi-equivalent interactions within hexamers and pentamers. The structures also clarify the molecular basis for capsid assembly inhibition and should facilitate structure-based drug design strategies.

  • Organizational Affiliation

    Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
A, B, C, D, E
A, B, C, D, E, F
342Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Synechocystis sp. PCC 6803 substr. Kazusa
This entity is chimeric
Mutation(s): 2 
Gene Names: gagccmK4slr1839
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Find proteins for P73407 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73407 
Go to UniProtKB:  P73407
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP12493P73407
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 7.00 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.286 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.618α = 90
b = 156.437β = 100.35
c = 196.644γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2009-06-23 
  • Deposition Author(s): Kelly, B.N.

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-06
    Changes: Database references
  • Version 1.3: 2017-05-31
    Changes: Structure summary
  • Version 1.4: 2017-06-21
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2017-11-01
    Changes: Refinement description
  • Version 1.6: 2024-02-21
    Changes: Data collection, Database references