7LY3 image
Entry Detail
PDB ID:
7LY3
Title:
Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab
Biological Source:
PDB Version:
Deposition Date:
2021-03-05
Release Date:
2021-04-14
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.23
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:A, B
Chain Length:335
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Description:S2M28 Fab Light Chain
Chain IDs:D (auth: C), E
Chain Length:212
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:S2M28 Fab Heavy Chain
Chain IDs:C (auth: D), F
Chain Length:221
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation

Abstact

The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.

Legend

Protein

Chemical

Disease

Primary Citation of related structures