7LY2 image
Deposition Date 2021-03-05
Release Date 2021-04-14
Last Version Date 2024-11-06
Entry Detail
PDB ID:
7LY2
Title:
SARS-CoV-2 S/S2M11/S2M28 Global Refinement
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A, F (auth: B), K (auth: J)
Chain Length:1288
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:S2M11 Fab Light Chain variable region
Chain IDs:B (auth: D), G (auth: C), L (auth: K)
Chain Length:104
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:S2M11 Fab Heavy Chain variable region
Chain IDs:C (auth: E), H (auth: F), M
Chain Length:122
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:S2M28 Fab Heavy Chain variable region
Chain IDs:D (auth: H), I (auth: G), N
Chain Length:117
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:S2M28 Fab Light Chain variable region
Chain IDs:E (auth: L), J (auth: I), O
Chain Length:106
Number of Molecules:3
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.

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Primary Citation of related structures