3MGE | pdb_00003mge

X-ray Structure of Hexameric HIV-1 CA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.255 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

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 Biology 401: 985-995

  • DOI: https://doi.org/10.1016/j.jmb.2010.06.042
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 25.55 kDa 
  • Atom Count: 1,747 
  • Modeled Residue Count: 204 
  • Deposited Residue Count: 231 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein p24231Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)Mutation(s): 4 
Gene Names: CAgag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
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 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.313α = 90
b = 90.313β = 90
c = 56.527γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary