8DWA

Crystal structure of neutralizing antibody P1D9 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD)

Summary for 8DWA

• Entry DOI: 10.2210/pdb8dwa/pdb
• Descriptor: Spike protein S1, P1D9 Heavy chain, P1D9 Light chain, ... (4 entities in total)
• Functional Keywords: covid-19, sars-cov-2, viral protein, spike glycoprotein, receptor binding protein, rbd, neutralizing antibody, 10-28, fab, viral protein-immune system complex, viral protein/immune system
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 3
• Total formula weight: 66463.23

Authors

Reddem, E.R.,Shapiro, L. (deposition date: 2022-08-01, release date: 2022-12-07, Last modification date: 2024-11-06)

Primary citation

Luo, M.,Zhou, B.,Reddem, E.R.,Tang, B.,Chen, B.,Zhou, R.,Liu, H.,Liu, L.,Katsamba, P.S.,Au, K.K.,Man, H.O.,To, K.K.,Yuen, K.Y.,Shapiro, L.,Dang, S.,Ho, D.D.,Chen, Z.
Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2.
Emerg Microbes Infect, 12:2146538-2146538, 2023

PubMed Abstract: Increasing 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.

PubMed: 36354024
DOI: 10.1080/22221751.2022.2146538

Experimental method

X-RAY DIFFRACTION (3.2 Å)