6AY9 | pdb_00006ay9

Structure of the native full-length HIV-1 capsid protein in complex with CPSF6 peptide

• PDB DOI: https://doi.org/10.2210/pdb6AY9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-09-07 Released: 2018-09-12 
• Deposition Author(s): Gres, A.T., Kirby, K.A., Sarafianos, S.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization.

Gres, A.T., Kirby, K.A., McFadden, W.M., Du, H., Liu, D., Xu, C., Bryer, A.J., Perilla, J.R., Shi, J., Aiken, C., Fu, X., Zhang, P., Francis, A.C., Melikyan, G.B., Sarafianos, S.G.

(2023) Nat Commun 14: 5614-5614

• PubMed: 37699872 
• DOI: https://doi.org/10.1038/s41467-023-41197-7
• Primary Citation Related Structures: 
  6AY9, 6AYA, 6B2G, 6B2H, 6B2I, 6B2J, 6B2K


• PubMed Abstract: 
  

  HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CA _NTD -CA _NTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45A ^a α9-helices compared to WT, E45A/R132T, WT _PF74 , WT _Nup153 , and WT _CPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.

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Organizational Affiliation: 
• C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
Department of Chemistry, University of Missouri, Columbia, MO, USA.
Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
Children's Healthcare of Atlanta, Atlanta, GA, USA.
Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, USA.
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
Department of Physics & Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Department of Pathology, Immunology & Microbiology, Vanderbilt University Medical Center, Nashville, TN, USA.
Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA.
Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.
Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, UK.
Department of Biological Science, Florida State University, Tallahassee, FL, USA.
Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA.
Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA. [e-mail].
Children's Healthcare of Atlanta, Atlanta, GA, USA. [e-mail].
Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.82 kDa 
• Atom Count: 1,835 
• Modeled Residue Count: 230 
• Deposited Residue Count: 243 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 capsid protein	A	231	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cleavage and polyadenylation specificity factor subunit 6	B	12	Homo sapiens	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
IOD	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	I [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.675	α = 90
b = 92.675	β = 90
c = 58.042	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
Blu-Ice	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
Aimless	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Gres, A.T., Kirby, K.A., Sarafianos, S.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI120860

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary