(A) Deuterium exchange at t = 1 min deuterium exchange mapped onto the structure of S protein (shades of blue [low exchange] and red [high exchange]). (B) Per-residue root mean square fluctuation (RMSF) of the S protein mapped onto the surface of the S trimer. Deuterium exchange-based dynamics across N-terminal domain (NTD) (C), receptor binding domain (RBD) (D), and the S2 subunit (E). (i) Relative fractional deuterium uptake (RFU) plots of NTD, RBD, and the S2 subunit at 1 min (orange) and 10 min (black) deuterium exchange times, with pepsin digest fragments displayed from N to C-terminus (X-axis). Peptides are grouped into clusters indicated by brackets (X-axis) for ease of display. Individual peptides within each cluster are identifiable from the Supplementary Excel file, which lists clusters and each peptide within each cluster (Supplementary file 1: Table S1). (Also see Figure 2—figure supplement 2). (ii) Deuterium exchange maps on close-up of the structures of NTD (21–303), RBD (318–552), and the S2 subunit (821–1197). Peptides spanning NTD–RBD interaction sites (166–182, 213–223, 294–303, 318–325, 375–387, and 442–449) showing relatively high deuterium exchange at t = 1 min are highlighted. (iii) The first principal motion and RMSF values of backbone atoms on the NTD, RBD, and the S2 subunit. Residues with high RMSF are labeled. Different domains (fusion peptide [FP], heptad repeat 1 [HR1], central helix [CH], connector domain [CD], heptad repeat 1 [HR2]) showing domain-specific RFU changes are labeled. RFU values are tabulated in Figure 2—source data 1.