7YOW

Crystal structure of SARS-CoV-2 omicron variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab

7YOW の概要

• エントリーDOI: 10.2210/pdb7yow/pdb
• 関連するPDBエントリー: 7WN2 7WNB
• 分子名称: Fab Light chain, Fab Heavy chain, Spike protein S1, ... (4 entities in total)
• 機能のキーワード: spike, coronavirus omicron strain, viral protein, fab, viral protein-immune system complex, virus, immune system-viral protein complex, immune system/viral protein
• 由来する生物種: Homo sapiens; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 148037.49

構造登録者

Yamamoto, A.,Higashiura, A. (登録日: 2022-08-02, 公開日: 2023-04-19, 最終更新日: 2024-11-13)

主引用文献

Shitaoka, K.,Higashiura, A.,Kawano, Y.,Yamamoto, A.,Mizoguchi, Y.,Hashiguchi, T.,Nishimichi, N.,Huang, S.,Ito, A.,Ohki, S.,Kanda, M.,Taniguchi, T.,Yoshizato, R.,Azuma, H.,Kitajima, Y.,Yokosaki, Y.,Okada, S.,Sakaguchi, T.,Yasuda, T.
Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants.
Commun Biol, 6:395-395, 2023

PubMed Abstract: The decrease of antibody efficacy to mutated SARS-CoV-2 spike RBD explains the breakthrough infections and reinfections by Omicron variants. Here, we analyzed broadly neutralizing antibodies isolated from long-term hospitalized convalescent patients of early SARS-CoV-2 strains. One of the antibodies named NCV2SG48 is highly potent to broad SARS-CoV-2 variants including Omicron BA.1, BA.2, and BA.4/5. To reveal the mode of action, we determined the sequence and crystal structure of the Fab fragment of NCV2SG48 in a complex with spike RBD from the original, Delta, and Omicron BA.1. NCV2SG48 is from a minor V but the multiple somatic hypermutations contribute to a markedly extended binding interface and hydrogen bonds to interact with conserved residues at the core receptor-binding motif of RBD, which efficiently neutralizes a broad spectrum of variants. Thus, eliciting the RBD-specific B cells to the longitudinal germinal center reaction confers potent immunity to broad SARS-CoV-2 variants emerging one after another.

PubMed: 37041231
DOI: 10.1038/s42003-023-04782-6

実験手法

X-RAY DIFFRACTION (3.3 Å)