9I8I | pdb_00009i8i

cryoEM structure of HIV-1 KAKA/G225R mature CA hexamer

• PDB DOI: https://doi.org/10.2210/pdb9I8I/pdb
• EM Map EMD-52724: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): HIV-1 06TG.HT008
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-05 Released: 2025-02-26 
• Deposition Author(s): Zhu, Y., Shen, J., Shen, Y., Xu, J., Zhang, P.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging.

Zhu, Y., Kleinpeter, A.B., Rey, J.S., Shen, J., Shen, Y., Xu, J., Hardenbrook, N., Chen, L., Lucic, A., Perilla, J.R., Freed, E.O., Zhang, P.

(2025) Nat Commun 16: 8152-8152

• PubMed: 40890096 
• DOI: https://doi.org/10.1038/s41467-025-63363-9
• Primary Citation Related Structures: 
  9I8I


• PubMed Abstract: 
  

  Inositol hexakisphosphate (IP6) promotes HIV-1 assembly by stabilizing the immature Gag lattice and becomes enriched within virions, where it is required for mature capsid assembly. Previously, we identified Gag mutants that package little IP6 yet assemble particles, though they are non-infectious due to defective capsid formation. Here, we report a compensatory mutation, G225R, in the C-terminus of capsid protein (CA) that restores capsid assembly and infectivity in these IP6-deficient mutants. G225R also enhances in vitro assembly of CA into capsid-like particles at far lower IP6 concentrations than required for wild-type CA. CryoEM structures of G225R CA hexamers and lattices at 2.7 Å resolution reveal that the otherwise disordered C-terminus becomes structured, stabilizing hexamer-hexamer interfaces. Molecular dynamics simulations support this mechanism. These findings uncover how HIV-1 can adapt to IP6 deficiency and highlight a previously unrecognized structural role of the CA C-terminus, while offering tools for capsid-related studies.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Institute for Advanced Study in Physics, Zhejiang University, Hangzhou, Zhejiang, China.
Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA. [e-mail].
Virus-Cell Interaction Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA. [e-mail].
Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. [e-mail].
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK. [e-mail].
Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 153.69 kDa 
• Atom Count: 10,374 
• Modeled Residue Count: 1,338 
• Deposited Residue Count: 1,386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 KAKA/G225R CA hexamer	A, B [auth F], C [auth E], D, E [auth C], F [auth B]	231	HIV-1 06TG.HT008	Mutation(s): 0
UniProt
Find proteins for D2ECD8 (HIV-1 M:B 2007_HIV_010) Explore D2ECD8  Go to UniProtKB:  D2ECD8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.75 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Zhu, Y., Shen, J., Shen, Y., Xu, J., Zhang, P.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release
  
• Version 1.1: 2025-03-05
  Changes: Data collection, Database references
• Version 1.2: 2026-04-01
  Changes: Data collection, Database references