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- EMDB-65164: Cryo-EM structure of SARS-CoV-2 XBB.1.5 S trimer in the early fus... -

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Entry
Database: EMDB / ID: EMD-65164
TitleCryo-EM structure of SARS-CoV-2 XBB.1.5 S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab (focused refinement of the S2-76E1 top)
Map data
Sample
  • Complex: the local S2-76E1 top map of the XBB.1.5 E-FIC-76E1 structure
KeywordsSpike / ACE2 / and 76E1-Fab complex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsLiu ZM / Bao ZH / Sun XY / Sun L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100751, 92469108 China
CitationJournal: Nature / Year: 2026
Title: Steric hindrance of antibody binding in an Omicron spike fusion intermediate.
Authors: Zhiheng Bao / Zhimin Liu / Zhaoyong Zhang / Xuanjia Wang / Xiaohui Jin / Jiaxiu Bai / Hanwen Ma / Yaxin Li / Chunyan Yi / Zhiyang Ling / Zhong Huang / Lu Zhang / Zhenguo Chen / Youhua Xie / ...Authors: Zhiheng Bao / Zhimin Liu / Zhaoyong Zhang / Xuanjia Wang / Xiaohui Jin / Jiaxiu Bai / Hanwen Ma / Yaxin Li / Chunyan Yi / Zhiyang Ling / Zhong Huang / Lu Zhang / Zhenguo Chen / Youhua Xie / Yanqun Wang / Lei Sun / Xiaoyu Sun /
Abstract: Understanding conformational changes of the coronavirus spike protein is critical for developing broad-spectrum therapies. The pan-coronavirus epitope spike residues 815-825 (centred on the S2' site) ...Understanding conformational changes of the coronavirus spike protein is critical for developing broad-spectrum therapies. The pan-coronavirus epitope spike residues 815-825 (centred on the S2' site) are buried in the prefusion spike but are transiently exposed upon ACE2 binding. Here, using integrated functional and structural analyses, we demonstrate that 76E1, an antibody targeting spike residues 815-825, specifically recognizes an open early fusion intermediate conformation in which this epitope adopts a helical conformation, designated the S2'-helix. SARS-CoV-2 Omicron variants evade such antibodies via steric hindrance resulting from S2'-helix shifts and restricted S1-ACE2 distancing in the early fusion intermediate conformation, together with increased reliance on cathepsin-mediated entry that impairs 76E1 inhibition of S2' cleavage. The H655Y mutation is central to this evasion. Antibody size directly affects its access to the S2'-helix. Crucially, antibody size minimization reversed the evasion mechanisms and significantly enhanced neutralizing activity against authentic Omicron variants and other human coronaviruses, including SARS-CoV-1 and HCoV-229E. These findings establish small-molecule targeting of the S2'-helix as a strategy for pan-coronavirus therapies.
History
DepositionJun 26, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65164.png

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Map

FileDownload / File: emd_65164.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372.8 Å		0.93 Å/pix.
x 400 pix.
= 372.8 Å		0.93 Å/pix.
x 400 pix.
= 372.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
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Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.0017477795 - 2.0171955
Average (Standard dev.)0.00093266106 (±0.020882161)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_65164_additional_1.map
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Half map: #1

Fileemd_65164_half_map_1.map
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Half map: #2

Fileemd_65164_half_map_2.map
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Sample components

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Entire : the local S2-76E1 top map of the XBB.1.5 E-FIC-76E1 structure

EntireName: the local S2-76E1 top map of the XBB.1.5 E-FIC-76E1 structure
Components
  • Complex: the local S2-76E1 top map of the XBB.1.5 E-FIC-76E1 structure

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Supramolecule #1: the local S2-76E1 top map of the XBB.1.5 E-FIC-76E1 structure

SupramoleculeName: the local S2-76E1 top map of the XBB.1.5 E-FIC-76E1 structure
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 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: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 29151
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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