Fig. 2: Atomically detailed pathways of spike opening.
From: A glycan gate controls opening of the SARS-CoV-2 spike protein
a–e, Snapshot configurations along the opening pathway with chain A shown in cyan, chain B in grey, chain C in pink and the glycan at position N343 in magenta. Each RBD and N-terminal ___domain (NTD) are subscripted with their chain ID (A, B or C). RBDs are also subscripted with their conformation from initial conformation with all three RBDs in the ‘down’ state (6VXX) (a), RBDA in a ‘transient’ state in between the ‘down’ and ‘up’ state (6VSB) (b) RBDA in the ‘up’ state (c), RBDA in the ‘open’ state (beyond 6VSB) (d) and RBDA in the furthest open state sampled (e). f, Scatter plot of data from the 310 continuous pathways with the Cα-root-mean-square deviation (RMSD) of the RBD from the RBDup state plotted against the RBD–core distance. Data points are coloured on the basis of the percentage RBD solvent-accessible surface area compared with the RBDdown state. The locations of the snapshots shown in a–e are labelled. g, Primary regions of spike defined for tracking progress of the opening transition. The spike core is composed of three central helices per trimer, coloured according to chains as in a–e. The RBD contains a structured pair of antiparallel beta-sheets, and an overlay of snapshots from a continuous WE simulation are shown coloured along a spectrum resembling the palette in f. Overlayed cryo-EM structures are highlighted and labelled including the initial RBDdown state (6VXX), the target RBDup state and the ACE2-bound RBDopen state (7A95).
