6VWS | pdb_00006vws

Hexamer of Helical HIV capsid by RASTR method

• PDB DOI: https://doi.org/10.2210/pdb6VWS/pdb
• EM Map EMD-21423: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-20 Released: 2020-10-21 
• Deposition Author(s): Zhao, H., Iqbal, N., Asturias, F., Kvaratskhelia, M., Vanblerkom, P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.08 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Starting Model: experimental

Literature

Structural and mechanistic bases for a potent HIV-1 capsid inhibitor.

Bester, S.M., Wei, G., Zhao, H., Adu-Ampratwum, D., Iqbal, N., Courouble, V.V., Francis, A.C., Annamalai, A.S., Singh, P.K., Shkriabai, N., Van Blerkom, P., Morrison, J., Poeschla, E.M., Engelman, A.N., Melikyan, G.B., Griffin, P.R., Fuchs, J.R., Asturias, F.J., Kvaratskhelia, M.

(2020) Science 370: 360-364

• PubMed: 33060363 
• DOI: https://doi.org/10.1126/science.abb4808
• Primary Citation Related Structures: 
  6VKV, 6VWS


• PubMed Abstract: 
  

  The potent HIV-1 capsid inhibitor GS-6207 is an investigational principal component of long-acting antiretroviral therapy. We found that GS-6207 inhibits HIV-1 by stabilizing and thereby preventing functional disassembly of the capsid shell in infected cells. X-ray crystallography, cryo-electron microscopy, and hydrogen-deuterium exchange experiments revealed that GS-6207 tightly binds two adjoining capsid subunits and promotes distal intra- and inter-hexamer interactions that stabilize the curved capsid lattice. In addition, GS-6207 interferes with capsid binding to the cellular HIV-1 cofactors Nup153 and CPSF6 that mediate viral nuclear import and direct integration into gene-rich regions of chromatin. These findings elucidate structural insights into the multimodal, potent antiviral activity of GS-6207 and provide a means for rationally developing second-generation therapies.

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Organizational Affiliation: 
• Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA.
Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA.
Department of Pediatrics, Infectious Diseases, Emory University, Atlanta, GA 30322, USA.
Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA. [e-mail] [e-mail].
Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA. [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 147.68 kDa 
• Atom Count: 6,510 
• Modeled Residue Count: 1,320 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV capsid protein	A, B, C, D, E [auth M], F [auth N]	220	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12493  Go to UniProtKB:  P12493

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.08 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.0
MODEL REFINEMENT	PHENIX	3758

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-10-21 
Deposition Author(s): Zhao, H., Iqbal, N., Asturias, F., Kvaratskhelia, M., Vanblerkom, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-67167
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI062520

Revision History  

• Version 1.0: 2020-10-21
  Type: Initial release
  
• Version 1.1: 2020-11-04
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Refinement description