Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Distinct Target Site of Lenacapavir in Immature HIV-1 and Concurrent Binding with the Maturation Inhibitor Bevirimat.
Journal, issue, pages	J Am Chem Soc, Vol. 147, Issue 46, Page 42685-42700, Year 2025
Publish date	Nov 19, 2025
Authors	Chunxiang Wu / Megan E Meuser / Juan S Rey / Hamed Meshkin / Rachel Yang / Swapnil C Devarkar / Christian Freniere / Jiong Shi / Christopher Aiken / Juan R Perilla / Yong Xiong /
PubMed Abstract	HIV-1 inhibitors, such as bevirimat (BVM) and lenacapavir (LEN), significantly reduce the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence ...HIV-1 inhibitors, such as bevirimat (BVM) and lenacapavir (LEN), significantly reduce the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high-resolution structures for BVM in complex with the immature Gag lattice and LEN's structural data being limited to the mature capsid. Utilizing perforated virus-like particles (VLPs) produced from mammalian cells, we determined in situ cryo-electron microscopy (cryo-EM) structures of HIV-1 with inhibitors. This allowed for the first structural determination of the native immature HIV-1 particle with BVM and LEN bound inside the VLPs at high resolutions. Our findings demonstrate that LEN not only binds the mature capsid but also targets the immature lattice in a distinct manner. The binding of LEN induces a conformational change in the capsid protein (CA) region and alters the architecture of the Gag lattice, which may affect the maturation process. In addition, a more accurate model of BVM engaging the Gag lattice is revealed, one that is independent of LEN binding. These insights expand our understanding of the inhibitory mechanisms of LEN and BVM on HIV-1 and provide valuable clues for the design of future inhibitors.
External links	J Am Chem Soc / PubMed:41198571 / PubMed Central
Methods	EM (single particle)
Resolution	2.1 - 3.18 Å
Structure data	45975 9cwv EMDB-45975, PDB-9cwv: Gag CA-SP1 immature lattice from intact enveloped virus-like particles Method: EM (single particle) / Resolution: 2.42 Å 46593 9d6c EMDB-46593, PDB-9d6c: Gag CA-SP1 immature lattice bound with Lenacapavir and Bevirimat from enveloped virus like particles Method: EM (single particle) / Resolution: 2.1 Å 46595 9d6e EMDB-46595, PDB-9d6e: Gag CA-SP1 immature lattice bound with Bevirimat from enveloped virus like particles Method: EM (single particle) / Resolution: 3.09 Å 46631 9d88 EMDB-46631, PDB-9d88: Gag CA-SP1 immature lattice from enveloped and perforated virus like particles Method: EM (single particle) / Resolution: 3.18 Å 47240 9dwd EMDB-47240, PDB-9dwd: Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles (T8I) Method: EM (single particle) / Resolution: 3.13 Å 47475 9e39 EMDB-47475, PDB-9e39: Gag CA-SP1 (T8I) immature lattice bound with Bevirimat from enveloped virus like particles Method: EM (single particle) / Resolution: 2.71 Å 71417 9p9l EMDB-71417, PDB-9p9l: Gag CA-SP1 immature lattice bound with Lenacapavir from enveloped virus like particles Method: EM (single particle) / Resolution: 2.28 Å 71418 9p9m EMDB-71418, PDB-9p9m: CA-SP1 immature lattice assembled in vitro with inhibitor lenacapavir (dialyzed to 50nM) Method: EM (single particle) / Resolution: 2.93 Å
Chemicals	ChemComp-IHP: INOSITOL HEXAKISPHOSPHATE ChemComp-HOH: WATER ChemComp-QNG: N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide / medication, antiretroviralYM ChemComp-2I4*: 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid
Source	human immunodeficiency virus type 1 group m subtype b (isolate hxb2) human immunodeficiency virus type 1 (new york-5 isolate) human immunodeficiency virus type 1 (hbx2 isolate)
Keywords	VIRUS LIKE PARTICLE / Gag / CA-SP1 / HIV-1 / Inhibitor / virion assembly / VIRAL PROTEIN