Structural and energetic profiling of SARS-CoV-2 receptor binding domain antibody recognition and the impact of circulating variants
Fig 1
Hierarchical clustering of SARS-CoV-2 RBD antibody binding modes.
(A) Pairwise root mean square distances (RMSDs) between heavy chain or nanobody binding orientations were determined for 70 antibody-RBD complex structures and used to perform hierarchical clustering. Boxes denote clusters containing multiple antibodies at distance cutoff of 8 Å (shown as dashed horizontal black line), and dashed magenta square denotes co-clustered structures shown in panel (B). (B) Example of co-clustered antibodies S304 (PDB code 7JX3) [21] and EY6A (PDB code 6ZCZ) [22] with a shared RBD binding mode (2.2 Å heavy chain orientation RMSD). Structures are superposed by RBD (gray), and S304 and EY6A heavy and light chains are colored separately as indicated.