Fig. 2: Structure of Pangolin-CoV spike protein.

A EM density representation from the 2.9 Å map of Pangolin-CoV S viewed from down the three-fold axis (top panel) and in the orthogonal view (lower panel). The subunits are coloured in sea blue, golden and rosy brown. The white ovals identify the areas shown in molecular representation on the right. B Comparison of the RBD/RBD interface from the pangolin-CoV (left) and SARS-CoV-2 S (PDB: 6ZGE, right) highlighting the Arg417Lys substitution. C Comparison of the RBD-associated subdomains of the pangolin-CoV (golden) and closed form of SARS-CoV-2 (green) in the left hand panel, showing the different positioning of the 294–304 helix and the presence of the 615–640 helix-turn-helix in the pangolin structure and, in the right hand panel, the overlap of the same Pangolin-CoV S structure (golden) with the corresponding region from the RaTG13 (PDB: 6ZGF) (pink). D Comparison of (left) the NTD-associated subdomain of Pangolin-CoV (golden) with that of the closed form of SARS-CoV-2 (green) showing the different domain orientations between them; (right) the closed (green) and open (blue) conformations of the NTD-associated subdomain of SARS-CoV-2 showing that the shift in orientation of the NTD-associated subdomain on spike opening is in the opposite direction to the shift seen between the Pangolin-CoV and closed SARS-CoV-2 conformations shown in the left panel.