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Structure paper

TitlePathogen-sugar interactions revealed by universal saturation transfer analysis.
Journal, issue, pagesScience, Vol. 377, Issue 6604, Page eabm3125, Year 2022
Publish dateJul 22, 2022
AuthorsCharles J Buchanan / Ben Gaunt / Peter J Harrison / Yun Yang / Jiwei Liu / Aziz Khan / Andrew M Giltrap / Audrey Le Bas / Philip N Ward / Kapil Gupta / Maud Dumoux / Tiong Kit Tan / Lisa Schimaski / Sergio Daga / Nicola Picchiotti / Margherita Baldassarri / Elisa Benetti / Chiara Fallerini / Francesca Fava / Annarita Giliberti / Panagiotis I Koukos / Matthew J Davy / Abirami Lakshminarayanan / Xiaochao Xue / Georgios Papadakis / Lachlan P Deimel / Virgínia Casablancas-Antràs / Timothy D W Claridge / Alexandre M J J Bonvin / Quentin J Sattentau / Simone Furini / Marco Gori / Jiandong Huo / Raymond J Owens / Christiane Schaffitzel / Imre Berger / Alessandra Renieri / / James H Naismith / Andrew J Baldwin / Benjamin G Davis /
PubMed AbstractMany 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 ...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.
External linksScience / PubMed:35737812
MethodsEM (single particle)
Resolution2.27 - 2.49 Å
Structure data

14152

7qur

EMDB-14152, PDB-7qur:
SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry
Method: EM (single particle) / Resolution: 2.27 Å

14153

7qus

EMDB-14153, PDB-7qus:
SARS-CoV-2 Spike, C3 symmetry
Method: EM (single particle) / Resolution: 2.39 Å

EMDB-14154: SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C1 symmetry
Method: EM (single particle) / Resolution: 2.44 Å

EMDB-14155: SARS-CoV-2 Spike, C1 symmetry
Method: EM (single particle) / Resolution: 2.49 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-GE9:
2,3,5-tris(iodanyl)benzamide

ChemComp-SIA:
N-acetyl-alpha-neuraminic acid / Sialic acid

ChemComp-EIC:
LINOLEIC ACID / Linoleic acid

ChemComp-HOH:
WATER / Water

Source
  • severe acute respiratory syndrome coronavirus 2
  • enterobacteria phage t4 (virus)
KeywordsVIRAL PROTEIN / SARS-CoV-2 Spike

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