9E39 | pdb_00009e39

Gag CA-SP1 (T8I) immature lattice bound with Bevirimat from enveloped virus like particles

• PDB DOI: https://doi.org/10.2210/pdb9E39/pdb
• EM Map EMD-47475: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-10-23 Released: 2025-10-29 
• Deposition Author(s): Wu, C., Meuser, M.E., Xiong, Y.
• 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: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM

Wu, C., Meuser, M.E., Rey, J.S., Meshkin, H., Yang, R., Devarkar, S.C., Freniere, C., Shi, J., Aiken, C., Perilla, J.R., Xiong, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 18-mer - A18 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 460.25 kDa 
• Atom Count: 31,231 
• Modeled Residue Count: 3,960 
• Deposited Residue Count: 4,158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	231	HIV-1 M:B_HXB2R	Mutation(s): 1  Gene Names: gag
UniProt
Find proteins for P04591 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04591  Go to UniProtKB:  P04591

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	T [auth J]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
2I4 (Subject of Investigation/LOI)	S [auth D]	3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid C36 H56 O6 YJEJKUQEXFSVCJ-WRFMNRASSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.71 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Wu, C., Meuser, M.E., Xiong, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54 AI170791
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI178846

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release