Extended Data Fig. 4: Mapping mutations of the Delta variant and other variants of concern to the surface of the spike protein.

a, The spike protein trimer (Protein Data Bank code: 6XR8, corresponding to a closed spike trimer with all three RBDs in the ‘down’ conformation) is shown with its surface coloured according to domains: NTD in dark blue, RBD in green, the remainder of S1 in yellow and S2 in light blue. Interfaces between protomers were left white to help visualize the boundaries of the protomers. The three polypeptide chains in the trimer were arbitrarily defined as A, B and C. Surface patches corresponding to residues mutated in the Delta variant are coloured in red. The bottom panel has the front protomer (chain A) removed to show the trimer interface (buried regions in the trimer are in white). The mutations in Delta are labelled in the bottom panel. b, NTD shown in three orthogonal views. The left panel corresponds roughly to the orientation seen in chain B in a, and the middle panel shows a view from the back. The right panel shows a view from the top of the trimer. Mutations found in the main variants of concern are indicated. The mutations found in the Delta variant are in red. c, RBD shown in three orthogonal views, coloured according to solvent exposure in the context of the closed spike: green and white indicate exposed and buried surfaces, as in a. The ACE2-binding surface is coloured in pink. The left panel shows a view from the top of the trimer, and the middle panel a view from below. The right panels show a view down the ACE2-binding surface, highlighted in pink in the bottom panel. Mutations found in the main variants of concern are indicated. The mutations found in the Delta variant are in red. The ovals indicate the epitope regions of the four main classes of anti-RBD neutralizing antibodies. Note that the mutations on the RBD cluster all around the ACE2 patch. Panels were prepared with the PyMOL Molecular Graphics System, v.2.1 (Schrödinger).