7L2C image
Deposition Date 2020-12-16
Release Date 2021-02-10
Last Version Date 2024-11-20
Entry Detail
PDB ID:
7L2C
Title:
Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD)
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.65 Å
R-Value Free:
0.27
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A, B
Chain Length:342
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:2-51 heavy chain
Chain IDs:C (auth: H), E (auth: C)
Chain Length:227
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:2-51 light chain
Chain IDs:D (auth: L), F (auth: D)
Chain Length:215
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite.
Cell Host Microbe 29 819 ? (2021)
PMID: 33789084 DOI: 10.1016/j.chom.2021.03.005

Abstact

Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain (NTD) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD-directed antibodies. Here, we report cryo-EM and crystal structures for seven potent NTD-directed neutralizing antibodies in complex with spike or isolated NTD. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed that all seven antibodies target a common surface, bordered by glycans N17, N74, N122, and N149. This site-formed primarily by a mobile β-hairpin and several flexible loops-was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD-directed neutralizing antibodies appear to target a single supersite.

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