7T7B

Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing antibody ADI-62113 Fab

Summary for 7T7B

• Entry DOI: 10.2210/pdb7t7b/pdb
• Descriptor: Spike protein S1, ADI-62113 Fab heavy chain, ADI-62113 Fab light chain, ... (5 entities in total)
• Functional Keywords: cross-neutralizing antibody; yydrxg; sars-cov-2; adi-62113; sarbecovirus; pattern search; ighd3-22, immune system, immune system-viral protein complex, immune system/viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 3
• Total formula weight: 72163.34

Authors

Liu, H.,Wilson, I.A. (deposition date: 2021-12-14, release date: 2022-08-03, Last modification date: 2024-10-30)

Primary citation

Liu, H.,Kaku, C.I.,Song, G.,Yuan, M.,Andrabi, R.,Burton, D.R.,Walker, L.M.,Wilson, I.A.
Human antibodies to SARS-CoV-2 with a recurring YYDRxG motif retain binding and neutralization to variants of concern including Omicron.
Commun Biol, 5:766-766, 2022

PubMed Abstract: Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally identified a YYDRxG motif encoded by IGHD3-22 in CDR H3 that facilitates antibody targeting to a functionally conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences uncovered 100 such antibodies, many of which can neutralize SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to target sarbecoviruses including the Omicron variant. These findings suggest an epitope-targeting strategy to identify potent and broadly neutralizing antibodies for design of pan-sarbecovirus vaccines and antibody therapeutics.

PubMed: 35906394
DOI: 10.1038/s42003-022-03700-6

Experimental method

X-RAY DIFFRACTION (2.59 Å)