Interactive structural visualizations of mutational escape from three structural classes of anti-SARS-CoV-2 RBD antibodies and polyclonal plasma

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 monoclonal antibodies of three structural classes and polyclonal convalescent human sera.

These visualizations are built using dms-view. These experiments are described in this preprint, and raw data are available here. Monoclonal antibodies and polyclonal plasma were isolated from SARS-CoV-2 convalescent individuals, as described in Robbiani, et al. (2020).

Sites where mutations reduce binding are shown for each monoclonal antibody or polyclonal plasma, and are mapped to the ACE2-bound RBD structure (PDB 6M0J).

dms-view renderings for each monoclonal antibody’s escape mapped to the ACE2-bound RBD structure:

• ACE2-bound RBD

dms-view renderings for each antibody’s escape mapped to its respective antibody-bound spike trimer or isolated RBD structure (structures published in Barnes, et al. (2020a); Barnes, et al. (2020b); Shi, et al. (2020)). Some antibodies have more than one published structure:

• Class 1 antibodies (antibodies bound to “up” RBD):
  • C105 (6XCM) (2 RBDs “up”)
  • C105 (6XCN) (3 RBDs “up”)
  • LY-CoV016 (7C01)* (isolated RBD:Fab)
• Class 2 antibodies (antibodies bound to “down” or “up” RBDs):
  • C144 (7K90) (3 RBDs “down”)
  • C002 (7K8S) (3 RBDs “down”)
  • C002 (7K8T) (2 RBDs “down”)
  • C121 (7K8X) (2 RBDs “down”)
  • C121 (7K8Y) (1 RBD “down”)
• Class 3 antibodies (antibodies bound to “down” RBDs):
  • C135 (7K8Z) (2 RBDs “down”)
  • C110 (7K8V) (2 RBDs “down”)

dms-view renderings for each polyclonal plasma’s escape mapped to the ACE2-bound RBD structure:

• polyclonal plasma

dms-view links for a larger cohort of SARS-CoV-2 convalescent individuals from Greaney, et al. (2021) can be found here. These individuals were recruited for the HAARVI study in the Seattle, WA area.

*Results for LY-CoV016 were first reported in Starr et al. (2021).