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- EMDB-45978: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-45978
TitleLJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 35O22 Fab
Map datamain map
Sample
  • Complex: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 35O22 Fab
KeywordsNHP / rhesus macaque / gp120 interface / HIV / NFL / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsOzorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI157299 United States
CitationJournal: Immunity / Year: 2025
Title: Vaccination of nonhuman primates elicits a broadly neutralizing antibody lineage targeting a quaternary epitope on the HIV-1 Env trimer.
Authors: Fabian-Alexander Schleich / Shridhar Bale / Javier Guenaga / Gabriel Ozorowski / Monika Àdori / Xiaohe Lin / Xaquin Castro Dopico / Richard Wilson / Mark Chernyshev / Alma Teresia Cotgreave ...Authors: Fabian-Alexander Schleich / Shridhar Bale / Javier Guenaga / Gabriel Ozorowski / Monika Àdori / Xiaohe Lin / Xaquin Castro Dopico / Richard Wilson / Mark Chernyshev / Alma Teresia Cotgreave / Marco Mandolesi / Jocelyn Cluff / Esmeralda D Doyle / Leigh M Sewall / Wen-Hsin Lee / Shiyu Zhang / Sijy O'Dell / Brandon S Healy / Deuk Lim / Vanessa R Lewis / Elana Ben-Akiva / Darrell J Irvine / Nicole A Doria-Rose / Martin Corcoran / Diane Carnathan / Guido Silvestri / Ian A Wilson / Andrew B Ward / Gunilla B Karlsson Hedestam / Richard T Wyatt /
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 ...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.
History
DepositionJul 30, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45978.png

Downloads & links

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Map

FileDownload / File: emd_45978.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 400 pix.
= 402.08 Å		1.01 Å/pix.
x 400 pix.
= 402.08 Å		1.01 Å/pix.
x 400 pix.
= 402.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.06815593 - 0.17456695
Average (Standard dev.)0.0000827381 (±0.0073662186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 402.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45978_msk_1.map
Projections & Slices
AxesZYX

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Half map: half map A

Fileemd_45978_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_45978_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 3...

EntireName: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 35O22 Fab
Components
  • Complex: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 35O22 Fab

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Supramolecule #1: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 3...

SupramoleculeName: LJF-085 Fab in complex with HIV Env ZM233 NFL TD CC3+ dimer and 35O22 Fab
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human immunodeficiency virus 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Details: 20 mM Tris pH 7.4, 150 mM NaCl, 0.005 mM LMNG
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: local refinement / Number images used: 9652
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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