7YKJ image
Entry Detail
PDB ID:
7YKJ
EMDB ID:
Title:
Omicron RBDs bound with P3E6 Fab (one up and one down)
Biological Source:
PDB Version:
Deposition Date:
2022-07-22
Release Date:
2022-12-28
Method Details:
Experimental Method:
Resolution:
3.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:P3E6 heavy chain
Chain IDs:C (auth: A)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Chain IDs:A (auth: B), B (auth: C)
Chain Length:1205
Number of Molecules:2
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Description:P3E6 light chain
Chain IDs:D
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2.
Emerg Microbes Infect 12 2146538 2146538 (2023)
PMID: 36354024 DOI: 10.1080/22221751.2022.2146538

Abstact

ABSTRACTIncreasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis.

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Primary Citation of related structures