Sialic acid (Sia) at the cell surface is a putative SARS-CoV-2 co-receptor via interactions with Spike N-terminal domain (NTD), and Sia-based inhibitors have shown efficacy against SARS-CoV-2 in culture. However, protein:small-molecule complexes pose difficult cryo-EM targets because small ligands typically act in relatively poorly resolved peripheral regions, and structural details of Spike:Sia interactions via the highly flexible NTD remain elusive. Spike receptor-binding domain (RBD) binds linoleic acid (LA), which interacts with neighboring RBD to lock-in a closed trimer with rigid, well-resolved NTDs. While endogenous LA from certain expression systems serendipitously permits visualization of bound Sia, necessary and sufficient conditions for reliable extraction of this complex remain unclear.
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