8TC1

Cryo-EM Structure of Spike Glycoprotein from Civet Coronavirus 007 in Closed Conformation

Summary for 8TC1

• Entry DOI: 10.2210/pdb8tc1/pdb
• EMDB information: 41150
• Descriptor: Spike glycoprotein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: spike, glycoprotein, coronavirus, viral protein
• Biological source: Civet SARS CoV 007/2004
• Total number of polymer chains: 3
• Total formula weight: 385790.61

Authors

Bostina, M.,Hills, F.R.,Eruera, A.R. (deposition date: 2023-06-29, release date: 2024-05-01, Last modification date: 2024-11-13)

Primary citation

Hills, F.R.,Eruera, A.R.,Hodgkinson-Bean, J.,Jorge, F.,Easingwood, R.,Brown, S.H.J.,Bouwer, J.C.,Li, Y.P.,Burga, L.N.,Bostina, M.
Variation in structural motifs within SARS-related coronavirus spike proteins.
Plos Pathog., 20:e1012158-e1012158, 2024

PubMed Abstract: SARS-CoV-2 is the third known coronavirus (CoV) that has crossed the animal-human barrier in the last two decades. However, little structural information exists related to the close genetic species within the SARS-related coronaviruses. Here, we present three novel SARS-related CoV spike protein structures solved by single particle cryo-electron microscopy analysis derived from bat (bat SL-CoV WIV1) and civet (cCoV-SZ3, cCoV-007) hosts. We report complex glycan trees that decorate the glycoproteins and density for water molecules which facilitated modeling of the water molecule coordination networks within structurally important regions. We note structural conservation of the fatty acid binding pocket and presence of a linoleic acid molecule which are associated with stabilization of the receptor binding domains in the "down" conformation. Additionally, the N-terminal biliverdin binding pocket is occupied by a density in all the structures. Finally, we analyzed structural differences in a loop of the receptor binding motif between coronaviruses known to infect humans and the animal coronaviruses described in this study, which regulate binding to the human angiotensin converting enzyme 2 receptor. This study offers a structural framework to evaluate the close relatives of SARS-CoV-2, the ability to inform pandemic prevention, and aid in the development of pan-neutralizing treatments.

PubMed: 38805567
DOI: 10.1371/journal.ppat.1012158

Experimental method

ELECTRON MICROSCOPY (1.92 Å)