3GV2

X-ray Structure of Hexameric HIV-1 CA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 7 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.282 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

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: 10.1016/j.cell.2009.04.063
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24,Carbon dioxide-concentrating mechanism protein CcmK homolog 4
A, B, C, D, E, F
342Synechocystis sp. (strain PCC 6803 / Kazusa)Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
This entity is chimeric
Mutation(s): 2 
Gene Names: ccmK4, gag
Find proteins for P73407 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Go to UniProtKB:  P73407
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12493
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 7 Å
  • R-Value Free: 0.323 
  • R-Value Work: 0.282 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.618α = 90.00
b = 156.437β = 100.35
c = 196.644γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-03-30 
  • Released Date: 2009-06-23 
  • Deposition Author(s): Kelly, B.N.

Revision History 

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