8IFY

Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2

Summary for 8IFY

• Entry DOI: 10.2210/pdb8ify/pdb
• EMDB information: 35426
• Descriptor: Spike glycoprotein, Angiotensin-converting enzyme, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: complex, viral protein, viral protein-hydrolase complex, viral protein/hydrolase
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 5
• Total formula weight: 540107.70

Authors

Han, P.,Meng, Y.M.,Qi, J.X. (deposition date: 2023-02-20, release date: 2023-08-30, Last modification date: 2024-10-23)

Primary citation

Han, P.,Meng, Y.,Zhang, D.,Xu, Z.,Li, Z.,Pan, X.,Zhao, Z.,Li, L.,Tang, L.,Qi, J.,Liu, K.,Gao, G.F.
Structural basis of white-tailed deer, Odocoileus virginianus , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity.
J.Virol., 97:e0050523-e0050523, 2023

PubMed Abstract: SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD), became the first wildlife species infected on a large scale and might serve as a host reservoir for variants of concern (VOCs) in case no longer circulating in humans. In this study, we comprehensively assessed the binding of the WTD angiotensin-converting enzyme 2 (ACE2) receptor to the spike (S) receptor-binding domains (RBDs) from the SARS-CoV-2 prototype (PT) strain and multiple variants. We found that WTD ACE2 could be broadly recognized by all of the tested RBDs. We further determined the complex structures of WTD ACE2 with PT, Omicron BA.1, and BA.4/5 S trimer. Detailed structural comparison revealed the important roles of RBD residues on 486, 498, and 501 sites for WTD ACE2 binding. This study deepens our understanding of the interspecies transmission mechanisms of SARS-CoV-2 and further addresses the importance of constant monitoring on SARS-CoV-2 infections in wild animals. IMPORTANCE Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events.

PubMed: 37676003
DOI: 10.1128/jvi.00505-23

Experimental method

ELECTRON MICROSCOPY (2.55 Å)