8VXW | pdb_00008vxw

HIV-1 R18L CA pentamer from capsid-like particles assembled in 1 M NaCl

• PDB DOI: https://doi.org/10.2210/pdb8VXW/pdb
• EM Map EMD-43642: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-02-06 Released: 2025-12-31 
• Deposition Author(s): Schirra, R.T., Pornillos, O., Ganser-Pornillos, B.K.
• 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: 4.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Arg18 Substitutions Reveal the Capacity of the HIV-1 Capsid Protein for Non-Fullerene Assembly.

Schirra, R.T., Dos Santos, N.F.B., Ganser-Pornillos, B.K., Pornillos, O.

(2024) Viruses 16

• PubMed: 39066201 
• DOI: https://doi.org/10.3390/v16071038
• Primary Citation of Related Structures:  
  8VXV, 8VXW


• PubMed Abstract: 
  

  In the fullerene cone HIV-1 capsid, the central channels of the hexameric and pentameric capsomers each contain a ring of arginine (Arg18) residues that perform essential roles in capsid assembly and function. In both the hexamer and pentamer, the Arg18 rings coordinate inositol hexakisphosphate, an assembly and stability factor for the capsid. Previously, it was shown that amino-acid substitutions of Arg18 can promote pentamer incorporation into capsid-like particles (CLPs) that spontaneously assemble in vitro under high-salt conditions. Here, we show that these Arg18 mutant CLPs contain a non-canonical pentamer conformation and distinct lattice characteristics that do not follow the fullerene geometry of retroviral capsids. The Arg18 mutant pentamers resemble the hexamer in intra-oligomeric contacts and form a unique tetramer-of-pentamers that allows for incorporation of an octahedral vertex with a cross-shaped opening in the hexagonal capsid lattice. Our findings highlight an unexpected degree of structural plasticity in HIV-1 capsid assembly.

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Organizational Affiliation: 
• Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA.
Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 127.93 kDa 
• Atom Count: 5,020 
• Modeled Residue Count: 1,015 
• Deposited Residue Count: 1,155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A, B, C, D, E	231	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag-pol
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.40 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: 2025-12-31 
Deposition Author(s): Schirra, R.T., Pornillos, O., Ganser-Pornillos, B.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21-AI167756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54-AI170856

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release