8DTT image
Deposition Date 2022-07-26
Release Date 2022-11-23
Last Version Date 2024-11-20
Entry Detail
PDB ID:
8DTT
Keywords:
Title:
Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV93-03
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:COV93-03 heavy chain
Chain IDs:A, D (auth: E)
Chain Length:218
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:COV93-03 light chain
Chain IDs:B, E (auth: F)
Chain Length:217
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Spike protein S2' stem helix peptide
Gene (Uniprot):S
Chain IDs:C (auth: G), F (auth: J)
Chain Length:15
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Primary Citation

Abstact

Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.

Legend

Protein

Chemical

Disease

Primary Citation of related structures