7VYR image
Deposition Date 2021-11-15
Release Date 2022-03-02
Last Version Date 2024-10-16
Entry Detail
PDB ID:
7VYR
Title:
Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody Fab fragment
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.20 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:D27 heavy chain
Chain IDs:A (auth: H), D (auth: A)
Chain Length:252
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:D27 light chain
Chain IDs:B (auth: L), E (auth: B)
Chain Length:238
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:C (auth: R), F (auth: C)
Chain Length:262
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Primary Citation
Computational design of a neutralizing antibody with picomolar binding affinity for all concerning SARS-CoV-2 variants.
Mabs 14 2021601 2021601 (2022)
PMID: 35030983 DOI: 10.1080/19420862.2021.2021601

Abstact

Coronavirus disease 2019, caused by SARS-CoV-2, remains an on-going pandemic, partly due to the emergence of variant viruses that can "break-through" the protection of the current vaccines and neutralizing antibodies (nAbs), highlighting the needs for broadly nAbs and next-generation vaccines. We report an antibody that exhibits breadth and potency in binding the receptor-binding domain (RBD) of the virus spike glycoprotein across SARS coronaviruses. Initially, a lead antibody was computationally discovered and crystallographically validated that binds to a highly conserved surface of the RBD of wild-type SARS-CoV-2. Subsequently, through experimental affinity enhancement and computational affinity maturation, it was further developed to bind the RBD of all concerning SARS-CoV-2 variants, SARS-CoV-1 and pangolin coronavirus with pico-molar binding affinities, consistently exhibited strong neutralization activity against wild-type SARS-CoV-2 and the Alpha and Delta variants. These results identify a vulnerable target site on coronaviruses for development of pan-sarbecovirus nAbs and vaccines.

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