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- EMDB-48440: Cryo-EM structure of 3nv.2, a modified 426c SOSIP-based immunogen -

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Basic information

Entry
Database: EMDB / ID: EMD-48440
TitleCryo-EM structure of 3nv.2, a modified 426c SOSIP-based immunogen
Map data
Sample
  • Complex: HIV-1 Envelope protein
KeywordsHIV-1 / Envelope protein / Vaccine / Immunogen / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsGavor E / Gristick HB / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HIVRAD P01 AI100148 United States
Bill & Melinda Gates FoundationINV-002143 United States
CitationJournal: J Exp Med / Year: 2025
Title: Design and characterization of HIV-1 vaccine candidates to elicit antibodies targeting multiple epitopes.
Authors: Harry B Gristick / Harald Hartweger / Yoshiaki Nishimura / Edem Gavor / Kaito Nagashima / Nicholas S Koranda / Priyanthi N P Gnanapragasam / Leesa M Kakutani / Luisa N Segovia / Olivia K ...Authors: Harry B Gristick / Harald Hartweger / Yoshiaki Nishimura / Edem Gavor / Kaito Nagashima / Nicholas S Koranda / Priyanthi N P Gnanapragasam / Leesa M Kakutani / Luisa N Segovia / Olivia K Donau / Jennifer R Keeffe / Anthony P West / Malcolm A Martin / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: A primary goal in the development of an AIDS vaccine is the elicitation of broadly neutralizing antibodies (bNAbs) that protect against diverse HIV-1 strains. To this aim, germline-targeting ...A primary goal in the development of an AIDS vaccine is the elicitation of broadly neutralizing antibodies (bNAbs) that protect against diverse HIV-1 strains. To this aim, germline-targeting immunogens have been developed to activate bNAb precursors and initiate the induction of bNAbs. While most preclinical germline-targeting HIV-1 vaccine candidates only include a single bNAb precursor epitope, an effective HIV-1 vaccine will likely require bNAbs that target multiple epitopes on Env. Here, we report a newly designed germline-targeting Env SOSIP trimer, named 3nv.2, that presents three bNAb epitopes on Env: the CD4bs, V3, and V2 epitopes. 3nv.2 forms a stable trimeric Env and binds to bNAb precursors from each of the desired epitopes. Immunization experiments in rhesus macaques and mice demonstrate 3nv.2 elicits the combined effects of its parent immunogens. Our results provide proof of concept for using a germline-targeting immunogen presenting three or more bNAb epitopes and a framework to develop improved next-generation HIV-1 vaccine candidates.
History
DepositionDec 24, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48440.png

Downloads & links

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Map

FileDownload / File: emd_48440.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å		0.87 Å/pix.
x 360 pix.
= 313.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0417
Minimum - Maximum-0.18769829 - 0.35850847
Average (Standard dev.)0.00043458998 (±0.010931395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 313.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48440_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48440_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : HIV-1 Envelope protein

EntireName: HIV-1 Envelope protein
Components
  • Complex: HIV-1 Envelope protein

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Supramolecule #1: HIV-1 Envelope protein

SupramoleculeName: HIV-1 Envelope protein / type: complex / ID: 1 / Parent: 0
Details: Stabilized, soluble form of heterotrimeric membrane glycoprotein comprising gp120 and gp41 subunits
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 330 KDa

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMC4H11NO3Tris

Details: 150 mM NaCl, 20 mM Tris-HCl, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was purified and monodisperse.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k 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: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 45000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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