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TitleCryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipids.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 2972, Year 2025
Publish dateMar 26, 2025
AuthorsGašper Šolinc / Marija Srnko / Franci Merzel / Ana Crnković / Mirijam Kozorog / Marjetka Podobnik / Gregor Anderluh /
PubMed AbstractThe 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- ...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.
External linksNat Commun / PubMed:40140423 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.5 - 3.6 Å
Structure data

50057

9eym

EMDB-50057, PDB-9eym:
The structure of solubilized octameric pore of actinoporin Fav prepared on DOPC:sphingomyelin membranes
Method: EM (single particle) / Resolution: 2.6 Å

50058

9eyn

EMDB-50058, PDB-9eyn:
The structure of solubilized octameric pore of actinoporin Fav prepared on DOPC, cholesterol, sphingomyelin membranes
Method: EM (single particle) / Resolution: 3.06 Å

50059

9eyo

EMDB-50059, PDB-9eyo:
The structure of solubilized octameric pore of actinoporin Fav prepared on POPG, cholesterol, sphingomyelin membranes
Method: EM (single particle) / Resolution: 2.86 Å

EMDB-50060: The octameric pore of actinoporin Fav prepared on DOPC:sphingomyelin:cholesterol containing nanodiscs
Method: EM (single particle) / Resolution: 3.6 Å

PDB-9eyl:
dN53 deletion variant of monomeric Fav - actinoporin from Orbicella faveolata
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-144:
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM

ChemComp-HOH:
WATER

PDB-1h8m:
Solution structure of ykt6

ChemComp-CLR:
CHOLESTEROL

Source
  • orbicella faveolata (invertebrata)
KeywordsTOXIN / Actinoporin / Pore-forming toxin / Orbicella faveolata / Pore / Octamer / Transmembrane pore / Nanopore / cholesterol

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