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- EMDB-46048: HIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 pol... -

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Basic information

Entry
Database: EMDB / ID: EMD-46048
TitleHIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 polyclonal Fab (gp41-FP, gp41-base epitopes)
Map datamain map
Sample
  • Complex: HIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 polyclonal Fab (gp41-FP, gp41-base epitopes)
KeywordsNHP / rhesus macaque / polyclonal / HIV / NFL / EMPEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsSewall LM / Ozorowski 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
DepositionAug 2, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46048.png

Downloads & links

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Map

FileDownload / File: emd_46048.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
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AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 192 pix.
= 395.52 Å		2.06 Å/pix.
x 192 pix.
= 395.52 Å		2.06 Å/pix.
x 192 pix.
= 395.52 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.035450816 - 0.103104696
Average (Standard dev.)-0.00005219317 (±0.0045749815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 395.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_46048_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_46048_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 pol...

EntireName: HIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 polyclonal Fab (gp41-FP, gp41-base epitopes)
Components
  • Complex: HIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 polyclonal Fab (gp41-FP, gp41-base epitopes)

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Supramolecule #1: HIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 pol...

SupramoleculeName: HIV Env ZM233 NFL TD CC3+ trimer in complex with NHP #1,2,3,4 polyclonal Fab (gp41-FP, gp41-base epitopes)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.4 / Details: Tris-buffered saline
StainingType: NEGATIVE / Material: uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: PARLODION / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj


Details: coordinates converted to map using Chimera molmap
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 3400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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