4GW6

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The A128T Resistance Mutation Reveals Aberrant Protein Multimerization as the Primary Mechanism of Action of Allosteric HIV-1 Integrase Inhibitors.

Feng, L.Sharma, A.Slaughter, A.Jena, N.Koh, Y.Shkriabai, N.Larue, R.C.Patel, P.A.Mitsuya, H.Kessl, J.J.Engelman, A.Fuchs, J.R.Kvaratskhelia, M.

(2013) J.Biol.Chem. 288: 15813-15820

  • DOI: 10.1074/jbc.M112.443390
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a very promising new class of anti-HIV-1 agents that exhibit a multimodal mechanism of action by allosterically modulating IN multimerization and interfering with IN-lens epithelium-derived gro ...

    Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are a very promising new class of anti-HIV-1 agents that exhibit a multimodal mechanism of action by allosterically modulating IN multimerization and interfering with IN-lens epithelium-derived growth factor (LEDGF)/p75 binding. Selection of viral strains under ALLINI pressure has revealed an A128T substitution in HIV-1 IN as a primary mechanism of resistance. Here, we elucidated the structural and mechanistic basis for this resistance. The A128T substitution did not affect the hydrogen bonding between ALLINI and IN that mimics the IN-LEDGF/p75 interaction but instead altered the positioning of the inhibitor at the IN dimer interface. Consequently, the A128T substitution had only a minor effect on the ALLINI IC50 values for IN-LEDGF/p75 binding. Instead, ALLINIs markedly altered the multimerization of IN by promoting aberrant higher order WT (but not A128T) IN oligomers. Accordingly, WT IN catalytic activities and HIV-1 replication were potently inhibited by ALLINIs, whereas the A128T substitution in IN resulted in significant resistance to the inhibitors both in vitro and in cell culture assays. The differential multimerization of WT and A128T INs induced by ALLINIs correlated with the differences in infectivity of HIV-1 progeny virions. We conclude that ALLINIs primarily target IN multimerization rather than IN-LEDGF/p75 binding. Our findings provide the structural foundations for developing improved ALLINIs with increased potency and decreased potential to select for drug resistance.


    Organizational Affiliation

    Center for Retrovirus Research, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gag-Pol polyprotein
A
163Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARS
Query on ARS

Download SDF File 
Download CCD File 
A
ARSENIC
As
RBFQJDQYXXHULB-UHFFFAOYSA-N
 Ligand Interaction
LF2
Query on LF2

Download SDF File 
Download CCD File 
A
(2S)-[6-bromo-4-(4-chlorophenyl)-2-methylquinolin-3-yl](tert-butoxy)ethanoic acid
C22 H21 Br Cl N O3
UXIVWMINNPGARX-FQEVSTJZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LF2IC50: 170 - 200200 nM (99) BINDINGDB
LF2Kd: 150 nM (98) BINDINGDB
LF2IC50: 630 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.769α = 90.00
b = 72.769β = 90.00
c = 65.379γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
CrystalCleardata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-08
    Type: Database references
  • Version 1.2: 2013-06-19
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description