Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 25551.35 
• Atom Count: 1606 
• Residue Count: 231 
• Unique protein chains: 1

3MGE

X-ray Structure of Hexameric HIV-1 CA

• DOI: 10.2210/pdb3MGE/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate NY5)
• Expression System: Escherichia coli
• Mutation(s): 4 


• Deposited: 2010-04-05 Released: 2010-07-21 
• Deposition Author(s): Pornillos, O.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.255 
• R-Value Work: 0.230 

Literature

Disulfide Bond Stabilization of the Hexameric Capsomer of Human Immunodeficiency Virus.

Pornillos, O., Ganser-Pornillos, B.K., Banumathi, S., Hua, Y., Yeager, M.

(2010) J.Mol.Biol. 401: 985-995

• PubMed: 20600115 
• DOI: 10.1016/j.jmb.2010.06.042


• PubMed Abstract: 
  

The human immunodeficiency virus type 1 capsid is modeled as a fullerene cone that is composed of approximately 250 hexamers and 12 pentamers of the viral CA protein. Structures of CA hexamers have been difficult to obtain because the hexamer-stabilizing interactions are inherently weak, and CA tends to spontaneously assemble into capsid-like particles. Here, we describe a two-step biochemical strategy to obtain soluble CA hexamers for crystallization. First, the hexamer was stabilized by engineering disulfide cross-links (either A14C/E45C or A42C/T54C) between the N-terminal domains of adjacent subunits. Second, the cross-linked hexamers were prevented from polymerizing further into hyperstable capsid-like structures by mutations (W184A and M185A) that interfered with dimeric association between the C-terminal domains that link adjacent hexamers. The structures of two different cross-linked CA hexamers were nearly identical, and we combined the non-mutated portions of the structures to generate an atomic resolution model for the native hexamer. This hybrid approach for structure determination should be applicable to other viral capsomers and protein-protein complexes in general.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Capsid protein p24	A	231	Human immunodeficiency virus type 1 group M subtype B (isolate NY5)	Mutation(s): 4  Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Go to UniProtKB:  P12497

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.255 
• R-Value Work: 0.230 
• Space Group: P 6

Unit Cell:

Length (Å)	Angle (°)
a = 90.313	α = 90.00
b = 90.313	β = 90.00
c = 56.527	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-04-05 
• Released Date: 2010-07-21 
• Deposition Author(s): Pornillos, O.

Revision History 

• Version 1.0: 2010-07-21
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance