2M8P

The structure of the W184AM185A mutant of the HIV-1 capsid protein


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 480 
  • Conformers Submitted: 100 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Dynamics of Full-Length HIV-1 Capsid Protein in Solution.

Deshmukh, L.Schwieters, C.D.Grishaev, A.Ghirlando, R.Baber, J.L.Clore, G.M.

(2013) J.Am.Chem.Soc. 135: 16133-16147

  • DOI: 10.1021/ja406246z
  • Primary Citation of Related Structures:  2M8L, 2M8N

  • PubMed Abstract: 
  • The HIV-1 capsid protein plays a crucial role in viral infectivity, assembling into a cone that encloses the viral RNA. In the mature virion, the N-terminal domain of the capsid protein forms hexameric and pentameric rings, while C-terminal domain ho ...

    The HIV-1 capsid protein plays a crucial role in viral infectivity, assembling into a cone that encloses the viral RNA. In the mature virion, the N-terminal domain of the capsid protein forms hexameric and pentameric rings, while C-terminal domain homodimers connect adjacent N-terminal domain rings to one another. Structures of disulfide-linked hexamer and pentamer assemblies, as well as structures of the isolated domains, have been solved previously. The dimer configuration in C-terminal domain constructs differs in solution (residues 144-231) and crystal (residues 146-231) structures by ∼30°, and it has been postulated that the former connects the hexamers while the latter links pentamers to hexamers. Here we study the structure and dynamics of full-length capsid protein in solution, comprising a mixture of monomeric and dimeric forms in dynamic equilibrium, using ensemble simulated annealing driven by experimental NMR residual dipolar couplings and X-ray scattering data. The complexity of the system necessitated the development of a novel computational framework that should be generally applicable to many other challenging systems that currently escape structural characterization by standard application of mainstream techniques of structural biology. We show that the orientation of the C-terminal domains in dimeric full-length capsid and isolated C-terminal domain constructs is the same in solution, and we obtain a quantitative description of the conformational space sampled by the N-terminal domain relative to the C-terminal domain on the nano- to millisecond time scale. The positional distribution of the N-terminal domain relative to the C-terminal domain is large and modulated by the oligomerization state of the C-terminal domain. We also show that a model of the hexamer/pentamer assembly can be readily generated with a single configuration of the C-terminal domain dimer, and that capsid assembly likely proceeds via conformational selection of sparsely populated configurations of the N-terminal domain within the capsid protein dimer.


    Organizational Affiliation

    Laboratory of Chemical Physics and ‡Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24
A
231Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 480 
  • Conformers Submitted: 100 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references
  • Version 1.2: 2016-04-27
    Type: Database references, Structure summary