8G6O

HIV-1 capsid lattice bound to IP6 and Lenacapavir

  • Classification: VIRUS LIKE PARTICLE
  • Organism(s): Human immunodeficiency virus 1
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-02-15 Released: 2023-05-03 
  • Deposition Author(s): Highland, C.M., Dick, R.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States), Medical Research Council (MRC, United Kingdom)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into HIV-1 polyanion-dependent capsid lattice formation revealed by single particle cryo-EM.

Highland, C.M.Tan, A.Ricana, C.L.Briggs, J.A.G.Dick, R.A.

(2023) Proc Natl Acad Sci U S A 120: e2220545120-e2220545120

  • DOI: https://doi.org/10.1073/pnas.2220545120
  • Primary Citation of Related Structures:  
    8G6K, 8G6L, 8G6M, 8G6N, 8G6O

  • PubMed Abstract: 

    The HIV-1 capsid houses the viral genome and interacts extensively with host cell proteins throughout the viral life cycle. It is composed of capsid protein (CA), which assembles into a conical fullerene lattice composed of roughly 200 CA hexamers and 12 CA pentamers. Previous structural analyses of individual CA hexamers and pentamers have provided valuable insight into capsid structure and function, but detailed structural information about these assemblies in the broader context of the capsid lattice is lacking. In this study, we combined cryoelectron tomography and single particle analysis (SPA) cryoelectron microscopy to determine structures of continuous regions of the capsid lattice containing both hexamers and pentamers. We also developed a method of liposome scaffold-based in vitro lattice assembly ("lattice templating") that enabled us to directly study the lattice under a wider range of conditions than has previously been possible. Using this approach, we identified a critical role for inositol hexakisphosphate in pentamer formation and determined the structure of the CA lattice bound to the capsid-targeting antiretroviral drug GS-6207 (lenacapavir). Our work reveals key structural details of the mature HIV-1 CA lattice and establishes the combination of lattice templating and SPA as a robust strategy for studying retroviral capsid structure and capsid interactions with host proteins and antiviral compounds.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D, E
238Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12493
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI147890
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5U54AI150472-09
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54AI170855-01
National Science Foundation (NSF, United States)United StatesDMR-1719875
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/16

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2023-05-24
    Changes: Derived calculations