7LQ7 image
Deposition Date 2021-02-13
Release Date 2021-09-15
Last Version Date 2024-10-23
Entry Detail
PDB ID:
7LQ7
Keywords:
Title:
Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV503 and COVA1-16
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.40 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:A, B, E
Chain Length:205
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:CV503 heavy chain
Chain IDs:C, F, M (auth: H)
Chain Length:224
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:CV503 light chain
Chain IDs:D, G, H (auth: L)
Chain Length:216
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:COVA1-16 heavy chain
Chain IDs:I (auth: T), K (auth: P), L (auth: y)
Chain Length:232
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:COVA1-16 light chain
Chain IDs:J (auth: U), N (auth: Q), O (auth: z)
Chain Length:214
Number of Molecules:3
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation

Abstact

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern threatens the efficacy of existing vaccines and therapeutic antibodies and underscores the need for additional antibody-based tools that potently neutralize variants by targeting multiple sites of the spike protein. We isolated 216 monoclonal antibodies targeting SARS-CoV-2 from plasmablasts and memory B cells collected from patients with coronavirus disease 2019. The three most potent antibodies targeted distinct regions of the receptor binding domain (RBD), and all three neutralized the SARS-CoV-2 Alpha and Beta variants. The crystal structure of the most potent antibody, CV503, revealed that it binds to the ridge region of SARS-CoV-2 RBD, competes with the angiotensin-converting enzyme 2 receptor, and has limited contact with key variant residues K417, E484, and N501. We designed bispecific antibodies by combining nonoverlapping specificities and identified five bispecific antibodies that inhibit SARS-CoV-2 infection at concentrations of less than 1 ng/ml. Through a distinct mode of action, three bispecific antibodies cross-linked adjacent spike proteins using dual N-terminal domain–RBD specificities. One bispecific antibody was greater than 100-fold more potent than a cocktail of its parent monoclonals in vitro and prevented clinical disease in a hamster model at a dose of 2.5 mg/kg. Two bispecific antibodies in our panel comparably neutralized the Alpha, Beta, Gamma, and Delta variants and wild-type virus. Furthermore, a bispecific antibody that neutralized the Beta variant protected hamsters against SARS-CoV-2 expressing the E484K mutation. Thus, bispecific antibodies represent a promising next-generation countermeasure against SARS-CoV-2 variants of concern.

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Primary Citation of related structures