7TV2 | pdb_00007tv2

X-ray crystal structure of HIV-2 CA protein CTD

• PDB DOI: https://doi.org/10.2210/pdb7TV2/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Human immunodeficiency virus type 2 (ISOLATE ROD)
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-03 Released: 2023-05-17 
• Deposition Author(s): Shi, K., Aihara, H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: 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 - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 9.71 kDa 
• Atom Count: 683 
• Modeled Residue Count: 84 
• Deposited Residue Count: 88 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A	88	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: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.246 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.813	α = 90
b = 30.919	β = 90.56
c = 46.494	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Shi, K., Aihara, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37-AI064064
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35-GM118047

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description, Source and taxonomy