9D6C

Gag CA-SP1 immature lattice bound with Lenacapavir and Bevirimat from enveloped virus like particles


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM.

Wu, C.Meuser, M.E.Rey, J.S.Meshkin, H.Yang, R.Devarkar, S.C.Freniere, C.Shi, J.Aiken, C.Perilla, J.R.Xiong, Y.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.10.09.617473
  • Primary Citation of Related Structures:  
    9CWV, 9D6C, 9D6D, 9D6E, 9D88, 9DWD

  • PubMed Abstract: 

    HIV-1 inhibitors, such as Bevirimat (BVM) and Lenacapavir (LEN), block the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high-resolution structures for BVM complexes and LEN's structural data being limited to the mature capsid. Utilizing perforated virus-like particles (VLPs) produced from mammalian cells, we developed an approach to determine 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 offer a more accurate model of BVM engaging the Gag lattice and, importantly, 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. These insights expand our understanding of the inhibitory mechanisms of BVM and LEN on HIV-1 and provide valuable clues for the design of future inhibitors.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gag
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
232HIV-1 M:B_HXB2RMutation(s): 1 
Gene Names: gag
UniProt
Find proteins for P04591 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04591 
Go to UniProtKB:  P04591
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04591
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QNG (Subject of Investigation/LOI)
Query on QNG

Download Ideal Coordinates CCD File 
CA [auth F]
DA [auth G]
EA [auth H]
HA [auth I]
IA [auth J]
CA [auth F],
DA [auth G],
EA [auth H],
HA [auth I],
IA [auth J],
JA [auth K],
MA [auth L],
OA [auth M],
PA [auth N],
S [auth A],
SA [auth O],
T [auth B],
TA [auth P],
UA [auth Q],
W [auth C],
XA [auth R],
Y [auth D],
Z [auth E]
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
C39 H32 Cl F10 N7 O5 S2
BRYXUCLEHAUSDY-WEWMWRJBSA-N
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
BA [auth E]
GA [auth H]
LA [auth K]
NA [auth M]
RA [auth N]
BA [auth E],
GA [auth H],
LA [auth K],
NA [auth M],
RA [auth N],
V [auth B],
WA [auth R]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
2I4 (Subject of Investigation/LOI)
Query on 2I4

Download Ideal Coordinates CCD File 
AA [auth E]
FA [auth H]
KA [auth K]
QA [auth N]
U [auth B]
AA [auth E],
FA [auth H],
KA [auth K],
QA [auth N],
U [auth B],
VA [auth Q],
X [auth D]
3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid
C36 H56 O6
YJEJKUQEXFSVCJ-WRFMNRASSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21_5207
MODEL REFINEMENTCoot

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 StatesU54 AI170791
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI178846

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release