Table 1.
Antibody-bound complexes resolved by cryo-EM for SARS-CoV-2 spike mutants
| Binding domain (conformation) | Mechanism of action | SARS-CoV-2 Ab (PDB IDs)a | Mutation at “RRAR” | Epitope on SARS2 spikeb | Reference |
|---|---|---|---|---|---|
| RBD (up) | sterically hinders ACE2 binding | C105 (6XCN, 6XCM) | SGAG | D405,T415, G416, K417, Y421, Y453, F456, R457, K458, N460, Y473, A475, G476, F486, N487, G502, Y505 | Barnes et al., 2020 |
| RBD (down) | blocks ACE2-binding interface of RBD | 2-4 (6XEY) | GSAS | Y449, Y453, L455, F456, V483, E484, G485, F486, Y489, F490, L492, Q493, S494 | Liu et al., 2020 |
| RBD (up/down) distinct from ACE2 binding sites | Ab-dependent cell cytotoxicity and phagocytosis | S309 (6WPT, 6WPS) | SGAG | N334, L335, P337, G339, E340, N343, A344,T345, R346, K356, R357, S359, N360, C361, L441, N343 glycan | Pinto et al., 2020 |
| RBD (up) | blocks ACE2 binding and attachment to host cell | H014 (7CAI, 7CAC, 7CAB, 7CAK,7CAH) | GSAS | Y369, A372,S373, F374, S375, T376, F377, K378, C379, Y380, V382, S383, P384, T385, D405, V407, R408, A411, P412, Q414, N437, V503 | Lv et al., 2020b |
| NTD (up/down) | restrains S protein structural changes | 4A8 (7C2L) | GSAS | Y144, Y145, H146, K147, K150, W152, H245, R246, S247, Y248, L249 | Chi et al., 2020 |
| RBD/NTD (down) | blocks ACE2 binding | Ab23 (7BYR) | GSAS | G446, Y449, E484, G485, F486, Y489, F490, L492, Q493, S494, G496, Q498 N501, Y505, N165 glycan | Cao et al., 2020b |
| RBD | blocks the RBD | EY6A (6ZDH) | GSAS | Y369, F374, S375, T376, F377, K378, C379, Y380, G381, V382, S383, P384, T385, K386, D389, L390, F392, P412, G413, D427, D428, F429, T430 | Zhou et al., 2020a |
a
PDB IDs of the cryo-EM structures containing the indicated Ab are given in parentheses.
b
Epitope residues of SARS-CoV-2 within 4 Å distance of the antibody based on the first PDB ID listed in column 3.