8FZC | pdb_00008fzc

HIV-2 Gag Capsid from Immature Virus-like Particles

• PDB DOI: https://doi.org/10.2210/pdb8FZC/pdb
• EM Map EMD-29607: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Human immunodeficiency virus type 2 (ISOLATE ROD)
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-01-28 Released: 2023-06-07 
• Deposition Author(s): Talledge, N., Zhang, W., Mansky, L.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

HIV-2 Immature Particle Morphology Provides Insights into Gag Lattice Stability and Virus Maturation.

Talledge, N., Yang, H., Shi, K., Coray, R., Yu, G., Arndt, W.G., Meng, S., Baxter, G.C., Mendonca, L.M., Castano-Diez, D., Aihara, H., Mansky, L.M., Zhang, W.

(2023) J Mol Biol 435: 168143-168143

• PubMed: 37150290 
• DOI: https://doi.org/10.1016/j.jmb.2023.168143
• Primary Citation Related Structures: 
  7TV2, 8FZC


• PubMed Abstract: 
  

  Retrovirus immature particle morphology consists of a membrane enclosed, pleomorphic, spherical and incomplete lattice of Gag hexamers. Previously, we demonstrated that human immunodeficiency virus type 2 (HIV-2) immature particles possess a distinct and extensive Gag lattice morphology. To better understand the nature of the continuously curved hexagonal Gag lattice, we have used the single particle cryo-electron microscopy method to determine the HIV-2 Gag lattice structure for immature virions. The reconstruction map at 5.5 Å resolution revealed a stable, wineglass-shaped Gag hexamer structure with structural features consistent with other lentiviral immature Gag lattice structures. Cryo-electron tomography provided evidence for nearly complete ordered Gag lattice structures in HIV-2 immature particles. We also solved a 1.98 Å resolution crystal structure of the carboxyl-terminal domain (CTD) of the HIV-2 capsid (CA) protein that identified a structured helix 12 supported via an interaction of helix 10 in the absence of the SP1 region of Gag. Residues at the helix 10-12 interface proved critical in maintaining HIV-2 particle release and infectivity. Taken together, our findings provide the first 3D organization of HIV-2 immature Gag lattice and important insights into both HIV Gag lattice stabilization and virus maturation.

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Organizational Affiliation: 
• Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA. Electronic address: https://twitter.com/BioChemTalledge.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
BioEM Lab, Biozentrum, University of Basel - Basel, Switzerland.
Minnesota Supercomputing Institute, Office of the Vice President for Research, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota - Twin Cities, USA.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
Instituto Biofisika CSIC-UPV/EHU, Leioa, Bizkaia, Spain.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA.
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Comparative Molecular Biosciences Graduate Program, University of Minnesota - Twin Cities, St. Paul, MN 55108, USA; Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA. Electronic address: [e-mail].
Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA; Characterization Facility, College of Sciences and Engineering, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by UCSF CHIMERA 1.16_b42360. (software)

Biological Assembly Evidence: gel filtration, electron microscopy

Macromolecule Content 

• Total Structure Weight: 75.33 kDa 
• Atom Count: 5,274 
• Modeled Residue Count: 672 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spacer peptide 2	A, B, C	224	Human immunodeficiency virus type 2 (ISOLATE ROD)	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for P04590 (Human immunodeficiency virus type 2 subtype A (isolate ROD)) Explore P04590  Go to UniProtKB:  P04590

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Talledge, N., Zhang, W., Mansky, L.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	124279
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	118047
National Science Foundation (NSF, United States)	United States	DMR-2011401
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	124165
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	007097
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	150351
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	83196

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection, Refinement description