Source Data: Structure and inhibition of SARS-CoV-2 spike refolding in membranes

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein binds the receptor Angiotensin Converting Enzyme 2 (ACE2) and drives virus-host membrane fusion through refolding of its S2 domain. Whereas the S1 domain contains high sequence variability, the S2 domain is conserved and is a promising pan-betacoronavirus vaccine target. We applied cryo-electron tomography to capture intermediates of S2 refolding and understand inhibition by anti-S2 stem-helix antibodies. Subtomogram averaging revealed ACE2 dimers cross-linking spikes before transitioning into S2 intermediates, which were captured at various stages of refolding. Pan-betacoronavirus neutralizing antibodies targeting the S2 stem-helix bound to and inhibited refolding of spike prehairpin intermediates. Combined with molecular dynamics simulations, these structures elucidate the process of SARS-CoV-2 entry and reveal how pan-betacoronavirus S2-targeting antibodies neutralize infectivity by arresting prehairpin in..., See Supplementary Materials in the Manuscript, , # **Source Data: Structure and inhibition of SARS-CoV-2 spike refolding in membranes**

[https://doi.org/10.5061/dryad.ncjsxkt3h ](https://doi.org/10.5061/dryad.ncjsxkt3h)

This dataset contains excel sheets from biological assays, a summary excel document of all cryoET measurements (Spike angles and membrane distances), scripts used for data processing and visualization, and MD Simulation data. PDB files for simulated prehairpin intermediate atomic models are also included.

## **Description of the data and file structure**

### **Directory \"Grunstetal\_Biological\_Cryo\_PrehairpinModels\":**

-The folders \"Fig1_Virus-CellFusionAssays\", \"Fig4_pre-post_attachment_assays\", and \"Fig4_FigS9_Neutralization_CellStaining\" include excel sheets from biological assays in this manuscript (pre-post attachment assays, fusion assays, neutralization assays, cell surface staining).

-In the folder \"Prehairpin_PDBFiles\", PDB files for simulated prehairpin intermediate models shown in Figure 3 and Fig S8...