Fig. 5
The position of RBD decorating glycans in relation to the rest of the SARS-CoV-2 S trimer during down-to-up transition for the native (A) and oxidized (B) systems. Region III*, IV, and the rest of the RBD are illustrated in magenta, green, and yellow colors, respectively. The rest of the SARS-CoV-2 S trimer, is depicted in cyan color. The glycans N331A and N234B are represented in white using licorice representation. The modified Cys residues in the oxidized system (see text) are shown with VDW representation. To enhance clarity on the positions of the RBD, glycans, and (native/oxidized) Cys residues, the top views of both the initial (0 ns) and final (5 ns) states of each system are zoomed in. The position of the host cell receptor is indicated by a dashed circle.
