Interactive structural visualizations of comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human sera

Below are links to interactive visualizations of the effects of single mutations to the SARS-CoV-2 spike receptor-binding domain (RBD) on binding by polyclonal convalescent human sera. These visualizations are built using dms-view. These experiments are described in Greaney, et al. (2021), and raw data are available here.

Sites where mutations reduce binding by serum antibodies are shown for each serum, and are mapped to the ACE2-bound RBD structure (PDB 6M0J). At least two time points per individual were mapped, and each time point is shown separately.

dms-view renderings for all 23 sera mapped to the ACE2-bound RBD structure (static views shown in Figure S3):

• ACE2-bound RBD

dms-view renderings highlighting various observations on which mutations affect binding of serum antibodies to the RBD:

• Many sera are narrowly focused on just a few sites in the receptor-binding ridge of the receptor-binding motif, and specifically, sites F456 and E484, e.g., subject B (day 26).
• Some sera target a wider swath of the receptor-binding motif, including sites F456, E484, and the 443-450 loop, e.g., subject G (day 18).
• Binding of a few sera are also affected by mutations to the core RBD, e.g., subject J (day 15).
• Some sera are more broad and are not strongly affected by any single mutation, e.g., subject G (day 94).