7QUR

SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry

Summary for 7QUR

• Entry DOI: 10.2210/pdb7qur/pdb
• EMDB information: 14152
• Descriptor: Spike glycoprotein,Fibritin, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ... (8 entities in total)
• Functional Keywords: sars-cov-2 spike, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 3
• Total formula weight: 436406.53

Authors

Naismith, J.H.,Yang, Y.,Liu, J.W. (deposition date: 2022-01-18, release date: 2022-06-01, Last modification date: 2024-11-06)

Primary citation

Buchanan, C.J.,Gaunt, B.,Harrison, P.J.,Yang, Y.,Liu, J.,Khan, A.,Giltrap, A.M.,Le Bas, A.,Ward, P.N.,Gupta, K.,Dumoux, M.,Tan, T.K.,Schimaski, L.,Daga, S.,Picchiotti, N.,Baldassarri, M.,Benetti, E.,Fallerini, C.,Fava, F.,Giliberti, A.,Koukos, P.I.,Davy, M.J.,Lakshminarayanan, A.,Xue, X.,Papadakis, G.,Deimel, L.P.,Casablancas-Antras, V.,Claridge, T.D.W.,Bonvin, A.M.J.J.,Sattentau, Q.J.,Furini, S.,Gori, M.,Huo, J.,Owens, R.J.,Schaffitzel, C.,Berger, I.,Renieri, A.,Naismith, J.H.,Baldwin, A.J.,Davis, B.G.
Pathogen-sugar interactions revealed by universal saturation transfer analysis.
Science, 377:eabm3125-eabm3125, 2022

PubMed Abstract: Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an "end-on" manner. uSTA-guided modeling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis.

PubMed: 35737812
DOI: 10.1126/science.abm3125

Experimental method

ELECTRON MICROSCOPY (2.27 Å)