HIV-1 capsid C-terminal domain mutant (Y169S)

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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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 U S A 111: 8233

  • DOI: https://doi.org/10.1073/pnas.1401455111
  • Primary Citation of Related Structures:  
    4COC, 4COP, 4D1K

  • 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. 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;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
86Human immunodeficiency virus 1Mutation(s): 1 
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.56α = 90
b = 72.39β = 109.32
c = 35.7γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-04
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references
  • Version 1.2: 2014-08-27
    Changes: Other
  • Version 1.3: 2019-11-13
    Changes: Data collection, Database references, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Refinement description