9MXB image
Deposition Date 2025-01-17
Release Date 2025-09-10
Last Version Date 2025-09-17
Entry Detail
PDB ID:
9MXB
Keywords:
Title:
Crystal Structure of WT HIV-1 Reverse Transcriptase in Complex with 5-{2-[2-(2-oxo-4-sulfanylidene-3,4-dihydropyrimidin-1(2H)-yl)ethoxy] phenoxy}naphthalene-2-carbonitrile (JLJ648), a non-nucleoside inhibitor
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.37 Å
R-Value Free:
0.27
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Reverse transcriptase/ribonuclease H
Gene (Uniprot):gag-pol
Chain IDs:A
Chain Length:557
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:p51 RT
Gene (Uniprot):gag-pol
Chain IDs:B
Chain Length:428
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
TPO B THR modified residue
Primary Citation
Mechanistic basis for a novel dual-function Gag-Pol dimerizer potentiating CARD8 inflammasome activation and clearance of HIV-infected cells.
Npj Drug Discov 2 22 22 (2025)
PMID: 40904837 DOI: 10.1038/s44386-025-00025-2

Abstact

A strategy to functionally cure AIDS by eliminating latent HIV-1 reservoirs involves non-nucleoside reverse transcriptase inhibitors (NNRTIs) that promote pyroptosis of HIV-1 infected cells. These NNRTIs stimulate dimerization of the Gag-Pol polyprotein, resulting in premature HIV-1 protease (PR) dimerization and cleavage of intracellular CARD8. A unique cell-based high-throughput screen was developed to identify potent compounds activating the CARD8 inflammasome through Gag-Pol dimerization. Our in-house library of NNRTIs was evaluated, including a series of catechol diethers, which are potent, nontoxic antivirals. JLJ648 was identified as a promising dual-function antiviral and Gag-Pol dimerizer. Cryo-EM studies of HIV reverse transcriptase p66 bound to JLJ648 revealed populations of homodimers and, surprisingly, a homotetramer. This novel homotetramer structure resembling an 'infinity knot' revealed two JLJ648-bound homodimers forming an extensive interface and nucleated around a dimer of JLJ648 molecules. Structure-guided mutagenesis studies indicate that Gag-Pol homotetramerization may play a critical role in facilitating PR self-cleavage and triggering pyroptosis.

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Protein

Chemical

Disease

Primary Citation of related structures
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