8J5J

The crystal structure of bat coronavirus RsYN04 RBD bound to the antibody S43

Summary for 8J5J

• Entry DOI: 10.2210/pdb8j5j/pdb
• Descriptor: Spike protein S1, nano antibody S43, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: complex, viral protein/immune system, viral protein-immune system complex
• Biological source: Betacoronavirus sp.; More
• Total number of polymer chains: 2
• Total formula weight: 40844.67

Authors

Zhao, R.C.,Niu, S.,Han, P.,Qi, J.X.,Gao, G.F.,Wang, Q.H. (deposition date: 2023-04-23, release date: 2023-11-22, Last modification date: 2024-11-13)

Primary citation

Zhao, R.,Niu, S.,Han, P.,Gao, Y.,Liu, D.,Luo, C.,Liu, H.,Liu, B.,Xu, Y.,Qi, J.,Chen, Z.,Shi, W.,Wu, L.,Gao, G.F.,Wang, Q.
Cross-species recognition of bat coronavirus RsYN04 and cross-reaction of SARS-CoV-2 antibodies against the virus.
Zool.Res., 44:1015-1025, 2023

PubMed Abstract: Following the outbreak of coronavirus disease 2019 (COVID-19), several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-related coronaviruses have been discovered. Previous research has identified a novel lineage of SARS-CoV-2-related CoVs in bats, including RsYN04, which recognizes human angiotensin-converting enzyme 2 (ACE2) and thus poses a potential threat to humans. Here, we screened the binding of the RsYN04 receptor-binding domain (RBD) to ACE2 orthologs from 52 animal species and found that the virus showed a narrower ACE2-binding spectrum than SARS-CoV-2. However, the presence of the T484W mutation in the RsYN04 RBD broadened its range. We also evaluated 44 SARS-CoV-2 antibodies targeting seven epitope communities in the SARS-CoV-2 RBD, together with serum obtained from COVID-19 convalescents and vaccinees, to determine their cross-reaction against RsYN04. Results showed that no antibodies, except for the RBD-6 and RBD-7 classes, bound to the RsYN04 RBD, indicating substantial immune differences from SARS-CoV-2. Furthermore, the structure of the RsYN04 RBD in complex with cross-reactive antibody S43 in RBD-7 revealed a potently broad epitope for the development of therapeutics and vaccines. Our findings suggest RsYN04 and other viruses belonging to the same clade have the potential to infect several species, including humans, highlighting the necessity for viral surveillance and development of broad anti-coronavirus countermeasures.

PubMed: 37804113
DOI: 10.24272/j.issn.2095-8137.2023.187

Experimental method

X-RAY DIFFRACTION (3 Å)