9Y7J | pdb_00009y7j

HIV-1 CA hexamer from purified viral cores bound to lenacapavir, C6 symmetry

• PDB DOI: https://doi.org/10.2210/pdb9Y7J/pdb
• EM Map EMD-72657: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-09-10 Released: 2026-02-25 
• Deposition Author(s): Barros dos Santos, N.F., Ganser-Pornillos, B.K., Pornillos, O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

HIV-1 CA hexamer from purified viral cores bound to lenacapavir, C6 symmetry

Barros dos Santos, N.F., Ganser-Pornillos, B.K., Pornillos, O.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 26.53 kDa 
• Atom Count: 1,726 
• Modeled Residue Count: 212 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A [auth L]	231	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol
UniProt
Find proteins for Q73368 (Human immunodeficiency virus type 1 group M subtype B (strain 89.6)) Explore Q73368  Go to UniProtKB:  Q73368

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QNG (Subject of Investigation/LOI)	B [auth L]	Lenacapavir C39 H32 Cl F10 N7 O5 S2 BRYXUCLEHAUSDY-WEWMWRJBSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.83 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Barros dos Santos, N.F., Ganser-Pornillos, B.K., Pornillos, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI150479
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54AI170856

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release