Unveiling the structural spectrum of SARS-CoV-2 fusion by in situ cryo-ET

DOI: 10.1038/s41467-025-60406-z

Authors: Caner Akil (Chinese Academy of Medical Sciences Oxford Institute, University of Oxford) , Jialu Xu (University of Oxford) , Juan Shen (University of Oxford) , Peijun Zhang (Chinese Academy of Medical Sciences Oxford Institute, University of Oxford; Diamond Light Source)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Nature Communications , VOL 16

State: Published (Approved)
Published: June 2025
Diamond Proposal Number(s): 29812

Abstract: SARS-CoV-2 entry into host cells is mediated by the spike protein, which drives membrane fusion. While cryo-EM reveals stable prefusion and postfusion conformations of the spike, the transient fusion intermediate states during the fusion process remain poorly understood. Here, we design a near-native viral fusion system that recapitulates SARS-CoV-2 entry and use cryo-electron tomography (cryo-ET) to capture fusion intermediates leading to complete fusion. The spike protein undergoes extensive structural rearrangements, progressing through extended, partially folded, and fully folded intermediates prior to fusion-pore formation, a process that depends on protease cleavage and is inhibited by the WS6 S2 antibody. Upon interaction with ACE2 receptor dimer, spikes cluster at membrane interfaces and following S2’ cleavage concurrently transition to postfusion conformations encircling the hemifusion and initial fusion pores in a distinct conical arrangement. S2’ cleavage is indispensable for advancing fusion intermediates to the fully folded postfusion state, culminating in membrane integration. Subtomogram averaging reveals that the WS6 S2 antibody binds to the spike’s stem-helix, crosslinks and clusters prefusion spikes, as well as inhibits refolding of fusion intermediates. These findings elucidate the entire process of spike-mediated fusion and SARS-CoV-2 entry, highlighting the neutralizing mechanism of S2-targeting antibodies.

Diamond Keywords: COVID-19; Viruses

Subject Areas: Biology and Bio-materials

Diamond Offline Facilities: Electron Bio-Imaging Centre (eBIC)
Instruments: Krios II-Titan Krios II at Diamond , Krios III-Titan Krios III at Diamond

Added On: 06/06/2025 08:08

Documents:
s41467-025-60406-z.pdf

Discipline Tags:

Pathogens Infectious Diseases Health & Wellbeing Structural biology Biophysics Life Sciences & Biotech

Technical Tags:

Imaging Tomography Cryo Electron Tomography (Cryo ET)