7SNQ | pdb_00007snq

Hexamer HIV-1 CA in complex with CPSF6 peptide and IP6 ligand

• PDB DOI: https://doi.org/10.2210/pdb7SNQ/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 BH10, Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-10-28 Released: 2022-09-07 
• Deposition Author(s): Bester, S.M., Kvaratskhelia, M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.282 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection.

Wei, G., Iqbal, N., Courouble, V.V., Francis, A.C., Singh, P.K., Hudait, A., Annamalai, A.S., Bester, S., Huang, S.W., Shkriabai, N., Briganti, L., Haney, R., KewalRamani, V.N., Voth, G.A., Engelman, A.N., Melikyan, G.B., Griffin, P.R., Asturias, F., Kvaratskhelia, M.

(2022) Nat Commun 13: 5879-5879

• PubMed: 36202818 
• DOI: https://doi.org/10.1038/s41467-022-33662-6
• Primary Citation Related Structures: 
  7SNQ


• PubMed Abstract: 
  

  Cellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short phenylalanine-glycine (FG) containing peptides with isolated capsid hexamers have been characterized, how these cellular factors functionally engage with biologically relevant mature HIV-1 capsid lattices is unknown. Here we show that prion-like low complexity regions (LCRs) enable avid CPSF6, NUP153 and SEC24C binding to capsid lattices. Structural studies revealed that multivalent CPSF6 assembly is mediated by LCR-LCR interactions, which are templated by binding of CPSF6 FG peptides to a subset of hydrophobic capsid pockets positioned along adjoining hexamers. In infected cells, avid CPSF6 LCR-mediated binding to HIV-1 cores is essential for functional virus-host interactions. The investigational drug lenacapavir accesses unoccupied hydrophobic pockets in the complex to potently impair HIV-1 inside the nucleus without displacing the tightly bound cellular cofactor from virus cores. These results establish previously undescribed mechanisms of virus-host interactions and antiviral action.

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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 & Molecular Genetics, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
Institute of Molecular Biophysics, Department of Biological Sciences, Florida State University, Tallahassee, FL, 32306, USA.
Department of Pediatrics, Emory University, Atlanta, GA, 30322, USA.
Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL, 60637, USA.
Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO, 80045, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B1C1D1E1F1G1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B1C1D1E1F1G1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 326.86 kDa 
• Atom Count: 20,569 
• Modeled Residue Count: 2,653 
• Deposited Residue Count: 2,952 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein p24	A, B, C, D, E, F, G, H, I, J, K, L	231	Human immunodeficiency virus type 1 BH10	Mutation(s): 4  Gene Names: gag-pol
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cleavage and polyadenylation specificity factor subunit 6	M, N, O, P, Q, R, S, T, U, V, W, X	15	Human immunodeficiency virus 1	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q16630 (Homo sapiens) Explore Q16630  Go to UniProtKB:  Q16630
PHAROS:  Q16630 GTEx:  ENSG00000111605

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP (Subject of Investigation/LOI)	BA [auth G], DA [auth K], Y [auth B], Z [auth E]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
CL	AA [auth E], CA [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.282 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.918	α = 90
b = 135.673	β = 90
c = 212.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Bester, S.M., Kvaratskhelia, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54 GM103368

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2022-10-19
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary