9EYN | pdb_00009eyn

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

PDB DOI: https://doi.org/10.2210/pdb9EYN/pdb
EM Map EMD-50058: EMDB EMDataResource

Classification: TOXIN
Organism(s): Orbicella faveolata
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-09 Released: 2025-04-23
Deposition Author(s): Solinc, G., Srnko, M., Svigel, T., Anderluh, G., Podobnik, M.
Funding Organization(s): Slovenian Research Agency, Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

Solinc, G., Srnko, M., Merzel, F., Crnkovic, A., Kozorog, M., Podobnik, M., Anderluh, G.

(2025) Nat Commun 16: 2972-2972

PubMed: 40140423 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-58334-z
Primary Citation Related Structures:
9EYL, 9EYM, 9EYN, 9EYO

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.

Organizational Affiliation

Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.

Macromolecule Content

Total Structure Weight: 295.51 kDa
Atom Count: 14,880
Modeled Residue Count: 1,448
Deposited Residue Count: 2,096
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actinoporin	A, B, C, D, E A, B, C, D, E, F, G, H	262	Orbicella faveolata	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H8M Query on A1H8M Download:Ideal Coordinates CCD File SDF format, chain ZC [auth H] SDF format, chain ZB [auth F] SDF format, chain ZA [auth D] SDF format, chain Z [auth B] SDF format, chain UC [auth G] SDF format, chain UB [auth E] SDF format, chain UA [auth C] SDF format, chain U [auth A] SDF format, chain TC [auth G] SDF format, chain TB [auth E] SDF format, chain TA [auth C] SDF format, chain T [auth A] SDF format, chain SC [auth G] SDF format, chain SB [auth E] SDF format, chain SA [auth C] SDF format, chain S [auth A] SDF format, chain RC [auth G] SDF format, chain RB [auth E] SDF format, chain RA [auth C] SDF format, chain R [auth A] SDF format, chain QC [auth G] SDF format, chain QB [auth E] SDF format, chain QA [auth C] SDF format, chain Q [auth A] SDF format, chain PC [auth G] SDF format, chain PB [auth E] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OC [auth G] SDF format, chain OB [auth E] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NC [auth G] SDF format, chain NB [auth E] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain MC [auth G] SDF format, chain MB [auth E] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain HD [auth H] SDF format, chain HC [auth F] SDF format, chain HB [auth D] SDF format, chain HA [auth B] SDF format, chain GD [auth H] SDF format, chain GC [auth F] SDF format, chain GB [auth D] SDF format, chain GA [auth B] SDF format, chain FD [auth H] SDF format, chain FC [auth F] SDF format, chain FB [auth D] SDF format, chain FA [auth B] SDF format, chain ED [auth H] SDF format, chain EC [auth F] SDF format, chain EB [auth D] SDF format, chain EA [auth B] SDF format, chain DD [auth H] SDF format, chain DC [auth F] SDF format, chain DB [auth D] SDF format, chain DA [auth B] SDF format, chain CD [auth H] SDF format, chain CC [auth F] SDF format, chain CB [auth D] SDF format, chain CA [auth B] SDF format, chain BD [auth H] SDF format, chain BC [auth F] SDF format, chain BB [auth D] SDF format, chain BA [auth B] SDF format, chain AD [auth H] SDF format, chain AC [auth F] SDF format, chain AB [auth D] SDF format, chain AA [auth B] MOL2 format, chain ZC [auth H] MOL2 format, chain ZB [auth F] MOL2 format, chain ZA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain UC [auth G] MOL2 format, chain UB [auth E] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth A] MOL2 format, chain TC [auth G] MOL2 format, chain TB [auth E] MOL2 format, chain TA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain SC [auth G] MOL2 format, chain SB [auth E] MOL2 format, chain SA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain RC [auth G] MOL2 format, chain RB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain QC [auth G] MOL2 format, chain QB [auth E] MOL2 format, chain QA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain PC [auth G] MOL2 format, chain PB [auth E] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OC [auth G] MOL2 format, chain OB [auth E] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NC [auth G] MOL2 format, chain NB [auth E] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain MC [auth G] MOL2 format, chain MB [auth E] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain HD [auth H] MOL2 format, chain HC [auth F] MOL2 format, chain HB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain GD [auth H] MOL2 format, chain GC [auth F] MOL2 format, chain GB [auth D] MOL2 format, chain GA [auth B] MOL2 format, chain FD [auth H] MOL2 format, chain FC [auth F] MOL2 format, chain FB [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain ED [auth H] MOL2 format, chain EC [auth F] MOL2 format, chain EB [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain DD [auth H] MOL2 format, chain DC [auth F] MOL2 format, chain DB [auth D] MOL2 format, chain DA [auth B] MOL2 format, chain CD [auth H] MOL2 format, chain CC [auth F] MOL2 format, chain CB [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain BD [auth H] MOL2 format, chain BC [auth F] MOL2 format, chain BB [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain AD [auth H] MOL2 format, chain AC [auth F] MOL2 format, chain AB [auth D] MOL2 format, chain AA [auth B] mmCIF format, chain ZC [auth H] mmCIF format, chain ZB [auth F] mmCIF format, chain ZA [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain UC [auth G] mmCIF format, chain UB [auth E] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth A] mmCIF format, chain TC [auth G] mmCIF format, chain TB [auth E] mmCIF format, chain TA [auth C] mmCIF format, chain T [auth A] mmCIF format, chain SC [auth G] mmCIF format, chain SB [auth E] mmCIF format, chain SA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain RC [auth G] mmCIF format, chain RB [auth E] mmCIF format, chain RA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain QC [auth G] mmCIF format, chain QB [auth E] mmCIF format, chain QA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain PC [auth G] mmCIF format, chain PB [auth E] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OC [auth G] mmCIF format, chain OB [auth E] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NC [auth G] mmCIF format, chain NB [auth E] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain MC [auth G] mmCIF format, chain MB [auth E] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain HD [auth H] mmCIF format, chain HC [auth F] mmCIF format, chain HB [auth D] mmCIF format, chain HA [auth B] mmCIF format, chain GD [auth H] mmCIF format, chain GC [auth F] mmCIF format, chain GB [auth D] mmCIF format, chain GA [auth B] mmCIF format, chain FD [auth H] mmCIF format, chain FC [auth F] mmCIF format, chain FB [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain ED [auth H] mmCIF format, chain EC [auth F] mmCIF format, chain EB [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain DD [auth H] mmCIF format, chain DC [auth F] mmCIF format, chain DB [auth D] mmCIF format, chain DA [auth B] mmCIF format, chain CD [auth H] mmCIF format, chain CC [auth F] mmCIF format, chain CB [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain BD [auth H] mmCIF format, chain BC [auth F] mmCIF format, chain BB [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain AD [auth H] mmCIF format, chain AC [auth F] mmCIF format, chain AB [auth D] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth D] AC [auth F] AD [auth H] BA [auth B] AA [auth B], AB [auth D], AC [auth F], AD [auth H], BA [auth B], BB [auth D], BC [auth F], BD [auth H], CA [auth B], CB [auth D], CC [auth F], CD [auth H], DA [auth B], DB [auth D], DC [auth F], DD [auth H], EA [auth B], EB [auth D], EC [auth F], ED [auth H], FA [auth B], FB [auth D], FC [auth F], FD [auth H], GA [auth B], GB [auth D], GC [auth F], GD [auth H], HA [auth B], HB [auth D], HC [auth F], HD [auth H], M [auth A], MA [auth C], MB [auth E], MC [auth G], N [auth A], NA [auth C], NB [auth E], NC [auth G], O [auth A], OA [auth C], OB [auth E], OC [auth G], P [auth A], PA [auth C], PB [auth E], PC [auth G], Q [auth A], QA [auth C], QB [auth E], QC [auth G], R [auth A], RA [auth C], RB [auth E], RC [auth G], S [auth A], SA [auth C], SB [auth E], SC [auth G], T [auth A], TA [auth C], TB [auth E], TC [auth G], U [auth A], UA [auth C], UB [auth E], UC [auth G], Z [auth B], ZA [auth D], ZB [auth F], ZC [auth H]	Sphingomyelin C18 C₄₁ H₈₄ N₂ O₆ P LKQLRGMMMAHREN-YJFXYUILSA-O		Interactions Focus chain AA [auth B] Focus chain AB [auth D] Focus chain AC [auth F] Focus chain AD [auth H] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain BD [auth H] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain CD [auth H] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain DD [auth H] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain ED [auth H] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth F] Focus chain FD [auth H] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GC [auth F] Focus chain GD [auth H] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth F] Focus chain HD [auth H] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain MC [auth G] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain NC [auth G] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain OC [auth G] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain PC [auth G] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain QC [auth G] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain RC [auth G] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain SC [auth G] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain TC [auth G] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain UC [auth G] Focus chain Z [auth B] Focus chain ZA [auth D] Focus chain ZB [auth F] Focus chain ZC [auth H] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth D] Focus chain AC [auth F] Focus chain AD [auth H] Focus chain BA [auth B] Focus chain BB [auth D] Focus chain BC [auth F] Focus chain BD [auth H] Focus chain CA [auth B] Focus chain CB [auth D] Focus chain CC [auth F] Focus chain CD [auth H] Focus chain DA [auth B] Focus chain DB [auth D] Focus chain DC [auth F] Focus chain DD [auth H] Focus chain EA [auth B] Focus chain EB [auth D] Focus chain EC [auth F] Focus chain ED [auth H] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain FC [auth F] Focus chain FD [auth H] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain GC [auth F] Focus chain GD [auth H] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain HC [auth F] Focus chain HD [auth H] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth E] Focus chain MC [auth G] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth E] Focus chain NC [auth G] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth E] Focus chain OC [auth G] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth E] Focus chain PC [auth G] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth E] Focus chain QC [auth G] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth E] Focus chain RC [auth G] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth E] Focus chain SC [auth G] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth E] Focus chain TC [auth G] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth E] Focus chain UC [auth G] Focus chain Z [auth B] Focus chain ZA [auth D] Focus chain ZB [auth F] Focus chain ZC [auth H]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain YC [auth H] SDF format, chain YB [auth F] SDF format, chain YA [auth D] SDF format, chain Y [auth B] SDF format, chain XC [auth H] SDF format, chain XB [auth F] SDF format, chain XA [auth D] SDF format, chain X [auth B] SDF format, chain WC [auth H] SDF format, chain WB [auth F] SDF format, chain WA [auth D] SDF format, chain W [auth B] SDF format, chain VC [auth H] SDF format, chain VB [auth F] SDF format, chain VA [auth D] SDF format, chain V [auth B] SDF format, chain LC [auth G] SDF format, chain LB [auth E] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KC [auth G] SDF format, chain KB [auth E] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JC [auth G] SDF format, chain JB [auth E] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain IC [auth G] SDF format, chain IB [auth E] SDF format, chain IA [auth C] SDF format, chain I [auth A] MOL2 format, chain YC [auth H] MOL2 format, chain YB [auth F] MOL2 format, chain YA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain XC [auth H] MOL2 format, chain XB [auth F] MOL2 format, chain XA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain WC [auth H] MOL2 format, chain WB [auth F] MOL2 format, chain WA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain VC [auth H] MOL2 format, chain VB [auth F] MOL2 format, chain VA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain LC [auth G] MOL2 format, chain LB [auth E] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KC [auth G] MOL2 format, chain KB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JC [auth G] MOL2 format, chain JB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain IC [auth G] MOL2 format, chain IB [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain I [auth A] mmCIF format, chain YC [auth H] mmCIF format, chain YB [auth F] mmCIF format, chain YA [auth D] mmCIF format, chain Y [auth B] mmCIF format, chain XC [auth H] mmCIF format, chain XB [auth F] mmCIF format, chain XA [auth D] mmCIF format, chain X [auth B] mmCIF format, chain WC [auth H] mmCIF format, chain WB [auth F] mmCIF format, chain WA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain VC [auth H] mmCIF format, chain VB [auth F] mmCIF format, chain VA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain LC [auth G] mmCIF format, chain LB [auth E] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KC [auth G] mmCIF format, chain KB [auth E] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JC [auth G] mmCIF format, chain JB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain IC [auth G] mmCIF format, chain IB [auth E] mmCIF format, chain IA [auth C] mmCIF format, chain I [auth A]	I [auth A] IA [auth C] IB [auth E] IC [auth G] J [auth A] I [auth A], IA [auth C], IB [auth E], IC [auth G], J [auth A], JA [auth C], JB [auth E], JC [auth G], K [auth A], KA [auth C], KB [auth E], KC [auth G], L [auth A], LA [auth C], LB [auth E], LC [auth G], V [auth B], VA [auth D], VB [auth F], VC [auth H], W [auth B], WA [auth D], WB [auth F], WC [auth H], X [auth B], XA [auth D], XB [auth F], XC [auth H], Y [auth B], YA [auth D], YB [auth F], YC [auth H]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain IC [auth G] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain JC [auth G] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain KC [auth G] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain LC [auth G] Focus chain V [auth B] Focus chain VA [auth D] Focus chain VB [auth F] Focus chain VC [auth H] Focus chain W [auth B] Focus chain WA [auth D] Focus chain WB [auth F] Focus chain WC [auth H] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain XC [auth H] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain YC [auth H] Interactions & Density Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain IC [auth G] Focus chain J [auth A] Focus chain JA [auth C] Focus chain JB [auth E] Focus chain JC [auth G] Focus chain K [auth A] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain KC [auth G] Focus chain L [auth A] Focus chain LA [auth C] Focus chain LB [auth E] Focus chain LC [auth G] Focus chain V [auth B] Focus chain VA [auth D] Focus chain VB [auth F] Focus chain VC [auth H] Focus chain W [auth B] Focus chain WA [auth D] Focus chain WB [auth F] Focus chain WC [auth H] Focus chain X [auth B] Focus chain XA [auth D] Focus chain XB [auth F] Focus chain XC [auth H] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain YB [auth F] Focus chain YC [auth H]