7YCN image
Entry Detail
PDB ID:
7YCN
Title:
Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab
Biological Source:
PDB Version:
Deposition Date:
2022-07-01
Release Date:
2023-02-01
Method Details:
Experimental Method:
Resolution:
2.85 Å
R-Value Free:
0.24
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:A (auth: J), D (auth: A), G (auth: B), J (auth: G)
Chain Length:195
Number of Molecules:4
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Description:IY-2A Fab heavy chain
Chain IDs:B (auth: K), E, H (auth: C), K (auth: H)
Chain Length:228
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:IY-2A Fab light chain
Chain IDs:C (auth: L), F, I (auth: D), L (auth: I)
Chain Length:216
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.
Nat Commun 14 311 311 (2023)
PMID: 36658148 DOI: 10.1038/s41467-023-35949-8

Abstact

Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.

Legend

Protein

Chemical

Disease

Primary Citation of related structures