7YOW image
Entry Detail
PDB ID:
7YOW
Title:
Crystal structure of SARS-CoV-2 omicron variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab
Biological Source:
PDB Version:
Deposition Date:
2022-08-02
Release Date:
2023-04-19
Method Details:
Experimental Method:
Resolution:
3.30 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Fab Heavy chain
Chain IDs:B (auth: H), E (auth: B)
Chain Length:230
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Fab Light chain
Chain IDs:A (auth: L), D (auth: A)
Chain Length:215
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:C (auth: R), F (auth: C)
Chain Length:224
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
Primary Citation
Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol 6 395 395 (2023)
PMID: 37041231 DOI: 10.1038/s42003-023-04782-6

Abstact

The decrease of antibody efficacy to mutated SARS-CoV-2 spike RBD explains the breakthrough infections and reinfections by Omicron variants. Here, we analyzed broadly neutralizing antibodies isolated from long-term hospitalized convalescent patients of early SARS-CoV-2 strains. One of the antibodies named NCV2SG48 is highly potent to broad SARS-CoV-2 variants including Omicron BA.1, BA.2, and BA.4/5. To reveal the mode of action, we determined the sequence and crystal structure of the Fab fragment of NCV2SG48 in a complex with spike RBD from the original, Delta, and Omicron BA.1. NCV2SG48 is from a minor VH but the multiple somatic hypermutations contribute to a markedly extended binding interface and hydrogen bonds to interact with conserved residues at the core receptor-binding motif of RBD, which efficiently neutralizes a broad spectrum of variants. Thus, eliciting the RBD-specific B cells to the longitudinal germinal center reaction confers potent immunity to broad SARS-CoV-2 variants emerging one after another.

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