5HOT

Structural Basis for Inhibitor-Induced Aggregation of HIV-1 Integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.309 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis for Inhibitor-Induced Aggregation of HIV Integrase.

Gupta, K.Turkki, V.Sherrill-Mix, S.Hwang, Y.Eilers, G.Taylor, L.McDanal, C.Wang, P.Temelkoff, D.Nolte, R.T.Velthuisen, E.Jeffrey, J.Van Duyne, G.D.Bushman, F.D.

(2016) PLoS Biol 14: e1002584-e1002584

  • DOI: 10.1371/journal.pbio.1002584
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The allosteric inhibitors of integrase (termed ALLINIs) interfere with HIV replication by binding to the viral-encoded integrase (IN) protein. Surprisingly, ALLINIs interfere not with DNA integration but with viral particle assembly late during HIV r ...

    The allosteric inhibitors of integrase (termed ALLINIs) interfere with HIV replication by binding to the viral-encoded integrase (IN) protein. Surprisingly, ALLINIs interfere not with DNA integration but with viral particle assembly late during HIV replication. To investigate the ALLINI inhibitory mechanism, we crystallized full-length HIV-1 IN bound to the ALLINI GSK1264 and determined the structure of the complex at 4.4 Å resolution. The structure shows GSK1264 buried between the IN C-terminal domain (CTD) and the catalytic core domain. In the crystal lattice, the interacting domains are contributed by two different dimers so that IN forms an open polymer mediated by inhibitor-bridged contacts; the N-terminal domains do not participate and are structurally disordered. Engineered amino acid substitutions at the inhibitor interface blocked ALLINI-induced multimerization. HIV escape mutants with reduced sensitivity to ALLINIs commonly altered amino acids at or near the inhibitor-bound interface, and these substitutions also diminished IN multimerization. We propose that ALLINIs inhibit particle assembly by stimulating inappropriate polymerization of IN via interactions between the catalytic core domain and the CTD and that understanding the interface involved offers new routes to inhibitor optimization.


    Organizational Affiliation

    Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A, B
291Human immunodeficiency virus 1Mutation(s): 2 
Gene Names: pol
EC: 2.7.7
Find proteins for Q72498 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q72498
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2SQ
Query on 2SQ

Download CCD File 
A, B
(2S)-tert-butoxy[4-(8-fluoro-5-methyl-3,4-dihydro-2H-chromen-6-yl)-2-methyl-1-oxo-1,2-dihydroisoquinolin-3-yl]ethanoic acid
C26 H28 F N O5
LDALHHGVIZRJPA-QHCPKHFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.40 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.309 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.06α = 90
b = 107.06β = 90
c = 243.49γ = 120
Software Package:
Software NamePurpose
CNSrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI 052845

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence