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- EMDB-73731: SARS-CoV-2 spike S2 in complex with antibody B3-1 -

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Basic information

Entry
Database: EMDB / ID: EMD-73731
TitleSARS-CoV-2 spike S2 in complex with antibody B3-1
Map data
Sample
  • Complex: SARS-CoV-2 spike S2 in complex with antibody B3-1
KeywordsSARS-CoV-2 / spike protein / antibody / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhou L / Hsieh C / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2026
Title: Structural and functional characterization of a conserved cryptic epitope on SARS-CoV-2 spike S2 subunit.
Authors: Ling Zhou / Ching-Lin Hsieh / Sarah R Leist / Emily Happy Miller / Andrew P Horton / Sophie R Shoemaker / Elizabeth C Gardner / John M Powers / Daniel R Boutz / Michael L Mallory / Connor M ...Authors: Ling Zhou / Ching-Lin Hsieh / Sarah R Leist / Emily Happy Miller / Andrew P Horton / Sophie R Shoemaker / Elizabeth C Gardner / John M Powers / Daniel R Boutz / Michael L Mallory / Connor M Mullins / Nicole V Johnson / Alexandra L Tse / Albert Wang / Kamyab Javanmardi / Lily E Adams / Jonathan Schisler / Susan Marqusee / Kartik Chandran / Ralph S Baric / Jimmy D Gollihar / Jason S McLellan /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive evolution since its emergence in 2019, underscoring the continuous need for vaccines and therapeutics effective ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone extensive evolution since its emergence in 2019, underscoring the continuous need for vaccines and therapeutics effective against multiple variants of concern (VOCs). The S2 subunit of the viral spike (S) glycoprotein is highly conserved among sarbecoviruses, making it an attractive target for broadly protective countermeasures. To elucidate the S2 antigenic landscape, we employed yeast surface display to isolate S2-targeted antibodies from COVID-19 convalescent donors. Biophysical characterization revealed that these S2 apex-directed antibodies preferentially bind to open spike conformations and a stabilized S2 construct but not to the closed, trimeric prefusion spike. Cryo-electron microscopy structures defined a cryptic epitope encompassing the upper helix and fusion peptide proximal region on S2. This epitope is conserved among sarbecoviruses but remains largely occluded in the closed prefusion conformation of the spikes. As a result, the antibodies exhibited weak neutralization activity against SARS-CoV-2 pseudoviruses, failed to neutralize authentic viruses, and did not provide protection in a lethal mouse challenge model using a mouse-adapted SARS-CoV-2 strain. These findings highlight a non-neutralizing epitope on S2 capable of eliciting antibodies during SARS-CoV-2 infection in humans and provide valuable reagents for probing S2 conformational dynamics and optimizing S2-based vaccine antigens.
History
DepositionNov 3, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73731.png

Downloads & links

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Map

FileDownload / File: emd_73731.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å		0.81 Å/pix.
x 384 pix.
= 311.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.5123291 - 0.67638797
Average (Standard dev.)0.00010218792 (±0.007840662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 311.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_73731_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_73731_half_map_2.map
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Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike S2 in complex with antibody B3-1

EntireName: SARS-CoV-2 spike S2 in complex with antibody B3-1
Components
  • Complex: SARS-CoV-2 spike S2 in complex with antibody B3-1

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Supramolecule #1: SARS-CoV-2 spike S2 in complex with antibody B3-1

SupramoleculeName: SARS-CoV-2 spike S2 in complex with antibody B3-1 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 301860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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