3DIK | pdb_00003dik

Pseudo-atomic model of the HIV-1 CA hexameric lattice

• PDB DOI: https://doi.org/10.2210/pdb3DIK/pdb
• EM Map EMD-1529: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-20 Released: 2008-09-16 
• Deposition Author(s): Ganser-Pornillos, B.K., Cheng, A., Yeager, M.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY

Starting Models: experimental

Literature

Structure of full-length HIV-1 CA: a model for the mature capsid lattice

Ganser-Pornillos, B.K., Cheng, A., Yeager, M.

(2007) Cell 131: 70-79

• PubMed: 17923088 
• DOI: https://doi.org/10.1016/j.cell.2007.08.018
• Primary Citation Related Structures: 
  3DIK


• PubMed Abstract: 
  

  The capsids of mature retroviruses perform the essential function of organizing the viral genome for efficient replication. These capsids are modeled as fullerene structures composed of closed hexameric arrays of the viral CA protein, but a high-resolution structure of the lattice has remained elusive. A three-dimensional map of two-dimensional crystals of the R18L mutant of HIV-1 CA was derived by electron cryocrystallography. The docking of high-resolution domain structures into the map yielded the first unambiguous model for full-length HIV-1 CA. Three important protein-protein assembly interfaces are required for capsid formation. Each CA hexamer is composed of an inner ring of six N-terminal domains and an outer ring of C-terminal domains that form dimeric linkers connecting neighboring hexamers. Interactions between the two domains of CA further stabilize the hexamer and provide a structural explanation for the mechanism of action of known HIV-1 assembly inhibitors.

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Organizational Affiliation: 
• The Scripps Research Institute, Department of Cell Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.5 kDa 
• Atom Count: 219 
• Modeled Residue Count: 219 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A	219	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 0  Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.7	α = 90
b = 92.7	β = 90
c = 110	γ = 120

EM Software:

Task	Software Package	Version
RECONSTRUCTION	MRC

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Ganser-Pornillos, B.K., Cheng, A., Yeager, M.

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-07-18
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Refinement description