Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural basis of white-tailed deer, , ACE2 recognizing all the SARS-CoV-2 variants of concern with high affinity.
Journal, issue, pages	J Virol, Vol. 97, Issue 9, Page e0050523, Year 2023
Publish date	Sep 28, 2023
Authors	Pu Han / Yumin Meng / Di Zhang / Zepeng Xu / Zhiyuan Li / Xiaoqian Pan / Zhennan Zhao / Linjie Li / Lingfeng Tang / Jianxun Qi / Kefang Liu / George F Gao /
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 ...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.
External links	J Virol / PubMed:37676003 / PubMed Central
Methods	EM (single particle)
Resolution	2.55 - 3.51 Å
Structure data	34727 8hfx EMDB-34727, PDB-8hfx: Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with white-tailed deer ACE2 Method: EM (single particle) / Resolution: 2.98 Å 34728 8hfy EMDB-34728, PDB-8hfy: SARS-CoV-2 Omicron BA.1 spike protein receptor-binding domain in complex with white-tailed deer ACE2 Method: EM (single particle) / Resolution: 3.21 Å 34729 8hfz EMDB-34729, PDB-8hfz: Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with white-tailed deer ACE2 Method: EM (single particle) / Resolution: 2.71 Å 34730 8hg0 EMDB-34730, PDB-8hg0: Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-binding domain in complex with white-tailed deer ACE2 Method: EM (single particle) / Resolution: 3.51 Å 35426 8ify EMDB-35426, PDB-8ify: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2 Method: EM (single particle) / Resolution: 2.55 Å 35427 8ifz EMDB-35427, PDB-8ifz: Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein receptor-binding domain in complex with white-tailed deer ACE2 Method: EM (single particle) / Resolution: 2.85 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-ZN: Unknown entry
Source	severe acute respiratory syndrome coronavirus 2 human immunodeficiency virus 1 odocoileus virginianus texanus (mammal) odocoileus virginianus (white-tailed deer)
Keywords	VIRAL PROTEIN / Complex / VIRAL PROTEIN/HYDROLASE / VIRAL PROTEIN-HYDROLASE complex