4COC

HIV-1 capsid C-terminal domain mutant (Y169L)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryo-Electron Microscopy of Tubular Arrays of HIV-1 Gag Resolves Structures Essential for Immature Virus Assembly.

Bharat, T.A.M.Castillo Menendez, L.R.Hagen, W.J.H.Lux, V.Igonet, S.Schorb, M.Schur, F.K.M.Krausslich, H.Briggs, J.A.G.

(2014) Proc.Natl.Acad.Sci.USA 111: 8233

  • DOI: 10.1073/pnas.1401455111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subseq ...

    The assembly of HIV-1 is mediated by oligomerization of the major structural polyprotein, Gag, into a hexameric protein lattice at the plasma membrane of the infected cell. This leads to budding and release of progeny immature virus particles. Subsequent proteolytic cleavage of Gag triggers rearrangement of the particles to form mature infectious virions. Obtaining a structural model of the assembled lattice of Gag within immature virus particles is necessary to understand the interactions that mediate assembly of HIV-1 particles in the infected cell, and to describe the substrate that is subsequently cleaved by the viral protease. An 8-Å resolution structure of an immature virus-like tubular array assembled from a Gag-derived protein of the related retrovirus Mason-Pfizer monkey virus (M-PMV) has previously been reported, and a model for the arrangement of the HIV-1 capsid (CA) domains has been generated based on homology to this structure. Here we have assembled tubular arrays of a HIV-1 Gag-derived protein with an immature-like arrangement of the C-terminal CA domains and have solved their structure by using hybrid cryo-EM and tomography analysis. The structure reveals the arrangement of the C-terminal domain of CA within an immature-like HIV-1 Gag lattice, and provides, to our knowledge, the first high-resolution view of the region immediately downstream of CA, which is essential for assembly, and is significantly different from the respective region in M-PMV. Our results reveal a hollow column of density for this region in HIV-1 that is compatible with the presence of a six-helix bundle at this position.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany;,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany;Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, 69120 Heidelberg, Germany; hans-georg.kraeusslich@med.uni-heidelberg.de john.briggs@embl.de.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany;Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany;Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, 69120 Heidelberg, Germany;,Unité de Virologie Structurale, Departement Virologie, Institut Pasteur, 75724 Paris, France; andUnité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, 75724 Paris, France.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany;Molecular Medicine Partnership Unit, European Molecular Biology Laboratory/Universitätsklinikum Heidelberg, Heidelberg, Germany; hans-georg.kraeusslich@med.uni-heidelberg.de john.briggs@embl.de.,Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, 69120 Heidelberg, Germany;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAPSID PROTEIN P24
A, B, C
86Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 1 
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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 100.480α = 90.00
b = 33.760β = 108.32
c = 77.730γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-06-25
    Type: Database references