Extended Data Table 1.
Anti-SARS-CoV-2 NAb classification and structural properties.
| Extended Table 1. Classification and structural properties of SARS-CoV-2 RBD-specific antibodies | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Antibody | Reference | IGHV (# of aa SHM) | CDRH3 length (aa)^ | IGLV (# of aa SHM) | CDRL3 length (aa)^ | IC50/IC90 (ng/mL)† | Potential IgG intra-spike binding§ | Contacts adjacent RBD | Structural Information | |
| Class 1: Blocks ACE2, accessibility of RBD epitope only in “up” conformation | ||||||||||
| C102 | this study | VH3–53 (2) | 11 | VK3–20 (0) | 9 | 34 / 143 | ??? | ??? | 3.0 A Fab-RBD | |
| C105 | Barnes, et al.1 | VH3–53 (0) | 12 | VL2–8 (1) | 11 | 26.1 / 134 | Yes | No | 3.4 A Fab-S. PDB 6XCM | |
| B38 | Wu, et al.2 | VH3–53 (1) | 9 | VK1–9 (2) | 10 | 117 / NA | ??? | ??? | 1.8 A Fab-RBD, PDB 7BZ5 | |
| CC12.3 | Yuan, et al.3 | VH3–53 (3) | 12 | VK3–20 (1) | 9 | 20 / NA | ??? | ??? | 2.9 A. Fab-RBD, PDB 6XC7 | |
| Class 2: Blocks ACE2, accessibility of RBD epitope in “up”/“down” conformations | ||||||||||
| C002 | this study | VH3–30 (1) | 17 | VK1–39 (1) | 9 | 8.9 / 37.6 | Yes | Yes | 3.4 A Fab-S | |
| C104 | this study | VH4–34 (6) | 17 | VK3–20 (3) | 9 | 23.3 / 140 | Yes | Yes | 3.7 A Fab-S | |
| C119 | this study | VH1–46 (1) | 20 | VL2–14 (3) | 11 | 9.1 / 97.8 | Yes | Yes | 3.5 A Fab-S | |
| C121 | this study | VH1–2 (2) | 22 | VL2–23 (0) | 10 | 6.7 / 22.3 | Yes | Yes | 3.6 A Fab-S | |
| C144 | this study | VH3–53 (3) | 25 | VL2–14 (1) | 10 | 6.9 / 29.7 | Yes | Yes | 3.3 A Fab-S | |
| COVA2–39 | Wu, et al.4 | VH3–53 (3) | 17 | VL2–23 (1) | 10 | 36 / NA | ??? | ??? | 1.7 A Fab-RBD, PDB 7JMP | |
| 5A6 | Wang, et al.5 | 75.5 / NA | Yes | Yes | 2.4 A Fab-S | |||||
| P2B-2F6 | Ju, et al.6 | VH4–38*02 (2) | 20 | VL2–8 (0) | 10 | 50 / NA | ??? | ??? | 2.9 A Fab-RBD, PDB 7BWJ | |
| Ab2–4 | Liu, et al.7 | VH1–2 (3) | 15 | VL2–8 (0) | 10 | 394 / NA | Yes | No | 3.2 A Fab-S, PDB 6XEY | |
| BD23 | Cao, et al.8 | VH7–4*02 (0) | 19 | VK1–5*03 (0) | 9 | 4800 / NA | No | No | 3.8 A Fab-S, PDB 7BYR | |
| Class 3: Does not overlap with ACE2 binding site, accessibility of RBD epitope in “up”/”down” conformations | ||||||||||
| C135 | this study | VH3–30 (4) | 12 | VK1–5 (3) | 9 | 16.6 / 48.9 | No | No | 3.5 A Fab-S | |
| S309 | Pinto, et al.9 | VH1–18 (6) | 20 | VK3–20 (3) | 8 | 79* / NA | No | No | 3.1 A Fab-S, PDB 6WPS | |
| C110 | this study | VH5–51 (2) | 21 | VK1–5 (3) | 9 | 18.4 / 77.3 | No | No | 3.8 A Fab-S | |
| REGN10987 | Hansen, et al.10 | VH3–30 (4) | 13 | VL2–14 (6) | 10 | 6.1 / NA | ??? | ??? | 3.9 A Fab-RBD, PDB 6XDG | |
| Class 4: Does not overlap with ACE2 binding site, accessibility of RBD epitope only in “up” conformation | ||||||||||
| CR3022 | Yuan, et al.11 | VH5–51 (8) | 12 | VK4–1 (3) | 9 | >10,000 / NA | ??? | ??? | 3.1 A Fab-RBD, PDB 6W41 | |
| COV1–16 | Liu, et al.12 | VH1–46 (1) | 20 | VK1–33 (3) | 10 | 130 / NA | ??? | ??? | 2.9 A Fab-RBD | |
| EY6A | Zhou, et al.13 | VH3–30*18 (3) | 14 | VK1–39 (0) | 10 | 70–20,000**/ NA | No | Yes | 3.7 A Fab-S, PDB 6ZDH | |
^
Average human antibody CDRH3 and CDRL3 lengths are 15 (CDRH3) and 9–10 (CDRL3) amino acids.
*
IC50 calculated against authentic SARS-CoV-2 virus.
**
IC50 varied depending on neutralization assay utilized.
†
Unknown IC90s indicated as NA (not available).
§
Potential for intra-spike crosslinking by an IgG binding to a single spike trimer was evaluated as described in the Methods.
??? Inference that cannot be made from a structure of a Fab bound to a RBD.
IGHV = Immunoglobulin heavy chain variable gene segment;
IGLV= Immunoglobulin light chain variable gene segment
V gene segments, somatic hypermutation (SHM) information, CDR lengths, IC50/IC90 values for NAbs in this study are from ref.14.