Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 25.55 kDa 
• Atom Count: 1747 
• Modelled Residue Count: 204 
• Deposited Residue Count: 231 
• Unique protein chains: 1

3MGE

X-ray Structure of Hexameric HIV-1 CA

• PDB DOI: 10.2210/pdb3MGE/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 

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
• Primary Citation of Related Structures:  
  3MGE


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A	231	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	Mutation(s): 4  Gene Names: CA, gag-pol 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)
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
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 
• Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.313	α = 90
b = 90.313	β = 90
c = 56.527	γ = 120

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: 2010-04-05 
• 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
  Changes: Version format compliance
• Version 1.2: 2021-10-06
  Changes: Database references, Derived calculations