7WSK

Crystal structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with civet ACE2

Summary for 7WSK

• Entry DOI: 10.2210/pdb7wsk/pdb
• Descriptor: Processed angiotensin-converting enzyme 2, Spike protein S1, alpha-D-mannopyranose-(1-3)-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
• Biological source: Paguma larvata (Masked palm civet); More
• Total number of polymer chains: 2
• Total formula weight: 96482.59

Authors

Huang, B.,Han, P.,Qi, J. (deposition date: 2022-01-29, release date: 2022-06-08, Last modification date: 2023-11-29)

Primary citation

Li, L.,Han, P.,Huang, B.,Xie, Y.,Li, W.,Zhang, D.,Han, P.,Xu, Z.,Bai, B.,Zhou, J.,Kang, X.,Li, X.,Zheng, A.,Zhang, R.,Qiao, S.,Zhao, X.,Qi, J.,Wang, Q.,Liu, K.,Gao, G.F.
Broader-species receptor binding and structural bases of Omicron SARS-CoV-2 to both mouse and palm-civet ACE2s.
Cell Discov, 8:65-65, 2022

PubMed Abstract: The Omicron variant of SARS-CoV-2 carries multiple unusual mutations, particularly in the receptor-binding domain (RBD) of the spike (S) protein. Moreover, host-adapting mutations, such as residues 493, 498, and 501, were also observed in the Omicron RBD, which indicates that it is necessary to evaluate the interspecies transmission risk of the Omicron variant. Herein, we evaluated the interspecies recognition of the Omicron BA.1 and Delta RBDs by 27 ACE2 orthologs, including humans. We found that Omicron BA.1 expanded its receptor binding spectra to palm-civet, rodents, more bats (least horseshoe bat and greater horseshoe bat) and lesser hedgehog tenrec. Additionally, we determined the cryo-electron microscopy (cryo-EM) structure of the Omicron BA.1 S protein complexed with mouse ACE2 (mACE2) and the crystal structure of Omicron RBD complexed with palm-civet ACE2 (cvACE2). Several key residues for the host range have been identified. These results suggest that surveillance should be enhanced on the Omicron variant for its broader-species receptor binding to prevent spillover and expansion of reservoir hosts for a prolonged pandemic.

PubMed: 35821014
DOI: 10.1038/s41421-022-00431-0

Experimental method

X-RAY DIFFRACTION (3.3 Å)