8HGM

Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11

Summary for 8HGM

• Entry DOI: 10.2210/pdb8hgm/pdb
• EMDB information: 34742
• Descriptor: Spike glycoprotein, NIV-11 Fab heavy chain, NIV-11 Fab light chain, ... (4 entities in total)
• Functional Keywords: complex, viral protein, 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: 190160.68

Authors

Moriyama, S.,Anraku, Y.,Muranishi, S.,Adachi, Y.,Kuroda, D.,Higuchi, Y.,Kotaki, R.,Tonouchi, K.,Yumoto, K.,Suzuki, T.,Kita, S.,Someya, T.,Fukuhara, H.,Kuroda, Y.,Yamamoto, T.,Onodera, T.,Fukushi, S.,Maeda, K.,Nakamura-Uchiyama, F.,Hashiguchi, T.,Hoshino, A.,Maenaka, K.,Takahashi, Y. (deposition date: 2022-11-15, release date: 2023-10-25, Last modification date: 2024-09-25)

Primary citation

Moriyama, S.,Anraku, Y.,Taminishi, S.,Adachi, Y.,Kuroda, D.,Kita, S.,Higuchi, Y.,Kirita, Y.,Kotaki, R.,Tonouchi, K.,Yumoto, K.,Suzuki, T.,Someya, T.,Fukuhara, H.,Kuroda, Y.,Yamamoto, T.,Onodera, T.,Fukushi, S.,Maeda, K.,Nakamura-Uchiyama, F.,Hashiguchi, T.,Hoshino, A.,Maenaka, K.,Takahashi, Y.
Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Nat Commun, 14:4198-4198, 2023

PubMed Abstract: SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.

PubMed: 37452031
DOI: 10.1038/s41467-023-39890-8

Experimental method

ELECTRON MICROSCOPY (3.4 Å)