9DMF | pdb_00009dmf

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

• PDB DOI: https://doi.org/10.2210/pdb9DMF/pdb

• 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)

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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

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

• PubMed: 40339576 
• DOI: https://doi.org/10.1016/j.immuni.2025.04.010
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA.
The Scripps Research Institute, Department of Integrative Structural and Computational Biology, La Jolla, CA, USA.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA.
MIT, Koch Institute for Integrative Cancer Research and Department of Biological Engineering, Cambridge, MA, USA.
MIT, Koch Institute for Integrative Cancer Research and Department of Biological Engineering, Cambridge, MA, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA.
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden. Electronic address: [e-mail].
The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.83 kDa 
• Atom Count: 3,781 
• Modeled Residue Count: 437 
• Deposited Residue Count: 441 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LJF-0085 Fab heavy chain	A [auth H]	227	Macaca mulatta	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LJF-0085 Fab light chain	B [auth L]	214	Macaca mulatta	Mutation(s): 0

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 = 53.457	α = 90
b = 65.355	β = 90
c = 133.257	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
XDS	data reduction
XDS	data scaling
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Lin, X., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI157299

Revision History  

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