Cryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipids

Gašper Šolinc, Marija Srnko, Franci Merzel, Ana Crnković, Mirijam Kozorog, Marjetka Podobnik () and Gregor Anderluh ()
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Gašper Šolinc: National Institute of Chemistry
Marija Srnko: National Institute of Chemistry
Franci Merzel: National Institute of Chemistry
Ana Crnković: National Institute of Chemistry
Mirijam Kozorog: National Institute of Chemistry
Marjetka Podobnik: National Institute of Chemistry
Gregor Anderluh: National Institute of Chemistry

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract The structure and function of membrane proteins depend on their interactions with lipids that constitute membranes. Actinoporins are α-pore-forming proteins that bind preferentially to sphingomyelin-containing membranes, where they oligomerize and form transmembrane pores. Through a comprehensive cryo-electron microscopic analysis of a pore formed by an actinoporin Fav from the coral Orbicella faveolata, we show that the octameric pore interacts with 112 lipids in the upper leaflet of the membrane, reveal the roles of lipids, and demonstrate that the actinoporin surface is suited for binding multiple receptor sphingomyelin molecules. When cholesterol is present in the membrane, it forms a cluster of four molecules associated with each protomer. Atomistic simulations support the structural data and reveal additional effects of the pore on the lipid membrane. These data reveal a complex network of protein-lipid and lipid-lipid interactions and an underrated role of lipids in the structure and function of transmembrane protein complexes.

Date: 2025
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DOI: 10.1038/s41467-025-58334-z

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