To obtain sufficient conformational diversity for our analysis of the s-glycoprotein trimer, we used the results of a 10 µs MD simulation conducted by the D. E. Shaw group, which started from the same cryo-EM structure of s-glycoprotein. This trajectory was clustered using the cpptraj 37 module of AmberTools 16 and a distance-based metric defined by the mass-weighted root-mean-square deviation (RMSD) of the backbone atoms of the residues surrounding the gorge of the S1 domain. The RMSD was calculated relative to the starting structure. All residues located within 20 Å of the centreline of the tunnel in the initial s-glycoprotein structure (calculated as described below; 565 in total) were included when calculating this metric. The hierarchical agglomerative clustering algorithm was used with averagelinkage, a minimum distance between clusters (epsilon) cut-off of 2.5, sieve 5, and a minimum of 5 clusters.