8KHC image
Deposition Date 2023-08-21
Release Date 2024-04-17
Last Version Date 2025-06-25
Entry Detail
PDB ID:
8KHC
Keywords:
Title:
SARS-CoV-2 Omicron spike in complex with 5817 Fab
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A, B, C
Chain Length:1120
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:Heavy chain of 5817 Fab
Chain IDs:D (auth: F), F (auth: H)
Chain Length:125
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Light chain of 5817 Fab
Chain IDs:E (auth: G), G (auth: J)
Chain Length:108
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Identification of a broad sarbecovirus neutralizing antibody targeting a conserved epitope on the receptor-binding domain.
Cell Rep 43 113653 113653 (2024)
PMID: 38175758 DOI: 10.1016/j.celrep.2023.113653

Abstact

Omicron, as the emerging variant with enhanced vaccine tolerance, has sharply disrupted most therapeutic antibodies. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belongs to the subgenus Sarbecovirus, members of which share high sequence similarity. Herein, we report one sarbecovirus antibody, 5817, which has broad-spectrum neutralization capacity against SARS-CoV-2 variants of concern (VOCs) and SARS-CoV, as well as related bat and pangolin viruses. 5817 can hardly compete with six classes of receptor-binding-domain-targeted antibodies grouped by structural classifications. No obvious impairment in the potency is detected against SARS-CoV-2 Omicron and subvariants. The cryoelectron microscopy (cryo-EM) structure of neutralizing antibody 5817 in complex with Omicron spike reveals a highly conserved epitope, only existing at the receptor-binding domain (RBD) open state. Prophylactic and therapeutic administration of 5817 potently protects mice from SARS-CoV-2 Beta, Delta, Omicron, and SARS-CoV infection. This study reveals a highly conserved cryptic epitope targeted by a broad sarbecovirus neutralizing antibody, which would be beneficial to meet the potential threat of pre-emergent SARS-CoV-2 VOCs.

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Primary Citation of related structures