9CLJ | pdb_00009clj

HIV-2 CA T=1 Icosahedron; assembled via lipid templating


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM.

Cook, M.Freniere, C.Wu, C.Lozano, F.Xiong, Y.

(2025) Cell Rep 44: 115245-115245

  • DOI: https://doi.org/10.1016/j.celrep.2025.115245
  • Primary Citation of Related Structures:  
    9CLJ, 9CNS, 9CNT, 9CNU, 9CNV

  • PubMed Abstract: 

    One of the striking features of human immunodeficiency virus (HIV) is the capsid, a fullerene cone comprised of pleomorphic capsid protein (CA) that shields the viral genome and recruits cofactors. Despite significant advances in understanding the mechanisms of HIV-1 CA assembly and host factor interactions, HIV-2 CA assembly remains poorly understood. By templating the assembly of HIV-2 CA on functionalized liposomes, we report high-resolution structures of the HIV-2 CA lattice, including both CA hexamers and pentamers, alone and with peptides of host phenylalanine-glycine (FG)-motif proteins Nup153 and CPSF6. While the overall fold and mode of FG-peptide binding is conserved with HIV-1, this study reveals distinctive features of the HIV-2 CA lattice, including differing structural character at regions of host factor interactions and divergence in the mechanism of formation of CA hexamers and pentamers. This study extends our understanding of HIV capsids and highlights an approach facilitating the study of lentiviral capsid biology.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein p24240Human immunodeficiency virus 2Mutation(s): 0 
Gene Names: gag-pol
UniProt
Find proteins for P18042 (Human immunodeficiency virus type 2 subtype A (isolate Ghana-1))
Explore P18042 
Go to UniProtKB:  P18042
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18042
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC

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 StatesT32GM008283
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54AI170791
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50AI150481

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release