Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 128.65 kDa 
• Atom Count: 7918 
• Residue Count: 1033 
• Unique protein chains: 1

3P05

X-ray structure of pentameric HIV-1 CA

• DOI: 10.2210/pdb3P05/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-09-27 Released: 2011-01-12 
• Deposition Author(s): Pornillos, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Atomic-level modelling of the HIV capsid.

Pornillos, O., Ganser-Pornillos, B.K., Yeager, M.

(2011) Nature 469: 424-427

• PubMed: 21248851 
• DOI: 10.1038/nature09640
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The mature capsids of human immunodeficiency virus type 1 (HIV-1) and other retroviruses are fullerene shells, composed of the viral CA protein, that enclose the viral genome and facilitate its delivery into new host cells. Retroviral CA proteins contain independently folded amino (N)- and carboxy (C)-terminal domains (NTD and CTD) that are connected by a flexible linker. The NTD forms either hexameric or pentameric rings, whereas the CTD forms symmetric homodimers that connect the rings into a hexagonal lattice. We previously used a disulphide crosslinking strategy to enable isolation and crystallization of soluble HIV-1 CA hexamers. Here we use the same approach to solve the X-ray structure of the HIV-1 CA pentamer at 2.5 Å resolution. Two mutant CA proteins with engineered disulphides at different positions (P17C/T19C and N21C/A22C) converged onto the same quaternary structure, indicating that the disulphide-crosslinked proteins recapitulate the structure of the native pentamer. Assembly of the quasi-equivalent hexamers and pentamers requires remarkably subtle rearrangements in subunit interactions, and appears to be controlled by an electrostatic switch that favours hexamers over pentamers. This study completes the gallery of substructures describing the components of the HIV-1 capsid and enables atomic-level modelling of the complete capsid. Rigid-body rotations around two assembly interfaces appear sufficient to generate the full range of continuously varying lattice curvature in the fullerene cone.

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Organizational Affiliation: 

Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 CA	A, B, C, D, E	231	Human immunodeficiency virus 1	Mutation(s): 4  Gene Names: CA, gag EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	A, B, C, D, E	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.266 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.723	α = 90
b = 130.308	β = 97.37
c = 81.831	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-27 
• Released Date: 2011-01-12 
Deposition Author(s): Pornillos, O.

Revision History 

• Version 1.0: 2011-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance