4XRQ

Disulfide stabilized HIV-1 CA hexamer 4mut (S41A, Q67H, V165I, L172I) in complex with PF-3450074


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

HIV-1 Resistance to the Capsid-Targeting Inhibitor PF74 Results in Altered Dependence on Host Factors Required for Virus Nuclear Entry.

Zhou, J.Price, A.J.Halambage, U.D.James, L.C.Aiken, C.

(2015) J.Virol. 89: 9068-9079

  • DOI: 10.1128/JVI.00340-15
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • During HIV-1 infection of cells, the viral capsid plays critical roles in reverse transcription and nuclear entry of the virus. The capsid-targeting small molecule PF74 inhibits HIV-1 at early stages of infection. HIV-1 resistance to PF74 is complex, ...

    During HIV-1 infection of cells, the viral capsid plays critical roles in reverse transcription and nuclear entry of the virus. The capsid-targeting small molecule PF74 inhibits HIV-1 at early stages of infection. HIV-1 resistance to PF74 is complex, requiring multiple amino acid substitutions in the viral CA protein. Here we report the identification and analysis of a novel PF74-resistant mutant encoding amino acid changes in both domains of CA, three of which are near the pocket where PF74 binds. Interestingly, the mutant virus retained partial PF74 binding, and its replication was stimulated by the compound. The mutant capsid structure was not significantly perturbed by binding of PF74; rather, the mutations inhibited capsid interactions with CPSF6 and Nup153 and altered HIV-1 dependence on these host factors and on TNPO3. Moreover, the replication of the mutant virus was markedly impaired in activated primary CD4(+) T cells and macrophages. Our results suggest that HIV-1 escapes a capsid-targeting small molecule inhibitor by altering the virus's dependence on host factors normally required for entry into the nucleus. They further imply that clinical resistance to inhibitors targeting the PF74 binding pocket is likely to be strongly limited by functional constraints on HIV-1 evolution.


    Organizational Affiliation

    Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom.,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA chris.aiken@vanderbilt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein p24
A
231Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 8 
Gene Names: gag
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12493
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1B0
Query on 1B0

Download SDF File 
Download CCD File 
A
N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
C27 H27 N3 O2
ACDFWSNAQWFRRF-VWLOTQADSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1B0Kd: 86 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 90.350α = 90.00
b = 90.350β = 90.00
c = 56.930γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2018-11-21
    Type: Data collection, Source and taxonomy