6AXW

Structure of the I124A mutant of the HIV-1 capsid protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Identification of a Structural Element in HIV-1 Gag Required for Virus Particle Assembly and Maturation.

Novikova, M.Adams, L.J.Fontana, J.Gres, A.T.Balasubramaniam, M.Winkler, D.C.Kudchodkar, S.B.Soheilian, F.Sarafianos, S.G.Steven, A.C.Freed, E.O.

(2018) MBio 9: --

  • DOI: 10.1128/mBio.01567-18
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Late in the HIV-1 replication cycle, the viral structural protein Gag is targeted to virus assembly sites at the plasma membrane of infected cells. The capsid (CA) domain of Gag plays a critical role in the formation of the hexameric Gag lattice in t ...

    Late in the HIV-1 replication cycle, the viral structural protein Gag is targeted to virus assembly sites at the plasma membrane of infected cells. The capsid (CA) domain of Gag plays a critical role in the formation of the hexameric Gag lattice in the immature virion, and, during particle release, CA is cleaved from the Gag precursor by the viral protease and forms the conical core of the mature virion. A highly conserved Pro-Pro-Ile-Pro (PPIP) motif (CA residues 122 to 125) [PPIP(122-125)] in a loop connecting CA helices 6 and 7 resides at a 3-fold axis formed by neighboring hexamers in the immature Gag lattice. In this study, we characterized the role of this PPIP(122-125) loop in HIV-1 assembly and maturation. While mutations P123A and P125A were relatively well tolerated, mutation of P122 and I124 significantly impaired virus release, caused Gag processing defects, and abolished infectivity. X-ray crystallography indicated that the P122A and I124A mutations induce subtle changes in the structure of the mature CA lattice which were permissive for in vitro assembly of CA tubes. Transmission electron microscopy and cryo-electron tomography demonstrated that the P122A and I124A mutations induce severe structural defects in the immature Gag lattice and abrogate conical core formation. Propagation of the P122A and I124A mutants in T-cell lines led to the selection of compensatory mutations within CA. Our findings demonstrate that the CA PPIP(122-125) loop comprises a structural element critical for the formation of the immature Gag lattice. IMPORTANCE Capsid (CA) plays multiple roles in the HIV-1 replication cycle. CA-CA domain interactions are responsible for multimerization of the Gag polyprotein at virus assembly sites, and in the mature virion, CA monomers assemble into a conical core that encapsidates the viral RNA genome. Multiple CA regions that contribute to the assembly and release of HIV-1 particles have been mapped and investigated. Here, we identified and characterized a Pro-rich loop in CA that is important for the formation of the immature Gag lattice. Changes in this region disrupt viral production and abrogate the formation of infectious, mature virions. Propagation of the mutants in culture led to the selection of second-site compensatory mutations within CA. These results expand our knowledge of the assembly and maturation steps in the viral replication cycle and may be relevant for development of antiviral drugs targeting CA.


    Organizational Affiliation

    Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA efreed@nih.gov.,Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine, Atlanta, Georgia, USA.,Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA.,Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA.,Faculty of Biology and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, United Kingdom.,Electron Microscopy Laboratory, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 capsid protein
A
230Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 1 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12493
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.189 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 92.611α = 90.00
b = 92.611β = 90.00
c = 57.954γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
Blu-Icedata collection
Aimlessdata scaling
REFMACrefinement
Aimlessdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI120860

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references
  • Version 1.2: 2018-10-31
    Type: Data collection, Database references
  • Version 1.3: 2018-11-14
    Type: Data collection, Database references
  • Version 1.4: 2019-02-20
    Type: Author supporting evidence, Data collection