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 9XQH | pdb_00009xqh

LEN-bound HIV-1 capsid lattice within intact VLPs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9XQH

This is version 1.0 of the entry. See complete history. 

Literature

Structural basis of lenacapavir-induced HIV-1 capsid defects during virion maturation.

Tanaka, H., Morita, R., Oka, T., Fukushima, M., Kita, S., Sasaki, M., Maenaka, K., Machida, S.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-77803-7
  • Primary Citation Related Structures: 
    43KN, 43KO, 9XQH

  • PubMed Abstract: 

    Long-acting lenacapavir (LEN) has emerged as a highly effective, potentially game-changing therapy for HIV treatment and prevention. Its mechanism of action in the early phase of HIV-1 replication, when the capsid directs key post-entry steps such as reverse transcription, nuclear import, and integration, has been well characterized. In contrast, its effects during the late phase of replication, when the capsid assembles and matures within budding virions, remain poorly understood. Here, we determine the cryo-electron microscopy structure of the mature HIV-1 capsid lattice assembled within virus-like particles in the presence of LEN. Our structural analyses reveal that LEN alters interhexamer interactions, perturbs the capsid lattice curvature, and thereby prevents the formation of a functional cone-shaped capsid. Biochemical analyses further demonstrate that LEN-containing cores lose reverse transcriptase because of compromised capsid integrity, whereas integrase and viral RNA remain associated. Functionally, viruses produced in the presence of LEN exhibit markedly reduced infectivity, low reverse transcription activity, and poor integration. Taken together, these findings provide mechanistic insights into the late-phase action of LEN and provide key directions for the design of future inhibitors.


  • Organizational Affiliation: 
    • Department of Structural Virology, National Institute of Global Health and Medicine, Japan Institute for Health Security, Tokyo, Japan.

Macromolecule Content 

  • Total Structure Weight: 153.7 kDa 
  • Atom Count: 4,992 
  • Modeled Residue Count: 1,248 
  • Deposited Residue Count: 1,386 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Capsid protein p24
A, B, C, D, E
A, B, C, D, E, F
231Human immunodeficiency virus 1Mutation(s): 2 
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: 4.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP25fk0410078
Japan Agency for Medical Research and Development (AMED)JapanJP25fk0310547
Japan Agency for Medical Research and Development (AMED)JapanJP25fk0310530
Japan Agency for Medical Research and Development (AMED)JapanJP25fk0310527
Japan Society for the Promotion of Science (JSPS)JapanJP25K02504
Other government22T003
Other government23A1017
Other government25A1014
Japan Agency for Medical Research and Development (AMED)JapanJP22ama121037
Japan Agency for Medical Research and Development (AMED)JapanJP243fa627005
Japan Society for the Promotion of Science (JSPS)JapanJP20H05873

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-07
    Type: Initial release