9EYM

The structure of solubilized octameric pore of actinoporin Fav prepared on DOPC:sphingomyelin membranes

This is a non-PDB format compatible entry.

Summary for 9EYM

• Entry DOI: 10.2210/pdb9eym/pdb
• Related: 9EYL 9EYN 9EYO
• EMDB information: 50057 50060
• Descriptor: Actinoporin, Sphingomyelin C18 (2 entities in total)
• Functional Keywords: actinoporin, pore-forming toxin, pore, octamer, transmembrane pore, toxin, nanopore
• Biological source: Orbicella faveolata
• Total number of polymer chains: 8
• Total formula weight: 265566.35

Authors

Solinc, G.,Srnko, M.,Svigel, T.,Anderluh, G.,Podobnik, M. (deposition date: 2024-04-09, release date: 2025-04-23, Last modification date: 2025-11-05)

Primary citation

Solinc, G.,Srnko, M.,Merzel, F.,Crnkovic, A.,Kozorog, M.,Podobnik, M.,Anderluh, G.
Cryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipids.
Nat Commun, 16:2972-2972, 2025

PubMed 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.

PubMed: 40140423
DOI: 10.1038/s41467-025-58334-z

Experimental method

ELECTRON MICROSCOPY (2.6 Å)