9DMF | pdb_00009dmf

Crystal structure of LJF-0085 Fab, a non-human primate antibody targets HIV-1 envelope protein

  • Classification: IMMUNE SYSTEM
  • Organism(s): Macaca mulatta
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-09-13 Released: 2025-07-23 
  • Deposition Author(s): Lin, X., Wilson, I.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

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

Vaccination of nonhuman primates elicits a broadly neutralizing antibody lineage targeting a quaternary epitope on the HIV-1 Env trimer.

Schleich, F.A.Bale, S.Guenaga, J.Ozorowski, G.Adori, M.Lin, X.Castro Dopico, X.Wilson, R.Chernyshev, M.Cotgreave, A.T.Mandolesi, M.Cluff, J.Doyle, E.D.Sewall, L.M.Lee, W.H.Zhang, S.O'Dell, S.Healy, B.S.Lim, D.Lewis, V.R.Ben-Akiva, E.Irvine, D.J.Doria-Rose, N.A.Corcoran, M.Carnathan, D.Silvestri, G.Wilson, I.A.Ward, A.B.Karlsson Hedestam, G.B.Wyatt, R.T.

(2025) Immunity 58: 1598-1613.e8

  • DOI: https://doi.org/10.1016/j.immuni.2025.04.010
  • Primary Citation of Related Structures:  
    9CU5, 9CU6, 9CV7, 9DMF

  • PubMed Abstract: 

    The elicitation of cross-neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) by vaccination remains a major challenge. Here, we immunized previously Env-immunized nonhuman primates with a series of near-native trimers that possessed N-glycan deletions proximal to the conserved CD4 binding site (CD4bs) to focus B cells to this region. Following heterologous boosting with fully glycosylated trimers, we detected tier 2 cross-neutralizing activity in the serum of several animals. Isolation of 185 matched heavy- and light-chain sequences from Env-binding memory B cells from an early responder identified a broadly neutralizing antibody lineage, LJF-0034, which neutralized nearly 70% of an 84-member HIV-1 global panel. High-resolution cryoelectron microscopy (cryo-EM) structures revealed a bifurcated binding mode that bridged the CD4bs to V3 across the gp120:120 interface on two adjacent protomers, evading the proximal N276 glycan impediment to the CD4bs, allowing neutralization breadth. This quaternary epitope defines a potential target for future HIV-1 vaccine development.


  • Organizational Affiliation
    • Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LJF-0085 Fab heavy chainA [auth H]227Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LJF-0085 Fab light chainB [auth L]214Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.457α = 90
b = 65.355β = 90
c = 133.257γ = 90
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XDSdata scaling
PHENIXrefinement

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 StatesAI157299

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release