9DOB | pdb_00009dob

Membrane-bound OlyA (E69A)/PlyB (Hinge-Lock) prepore focused refinement

PDB DOI: https://doi.org/10.2210/pdb9DOB/pdb
EM Map EMD-47078: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Pleurotus ostreatus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2024-09-18 Released: 2025-09-24
Deposition Author(s): Smothers, J., Chen, Z., Li, Y., Han, Y., Radhakrishnan, A.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, Leducq Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Visualization of the interaction between sphingomyelin and cholesterol in lipid bilayer membranes.

Smothers, J.C., Nguyen, C.H.B., Han, Y., Li, Y., Chen, Z., Radhakrishnan, A.

(2026) Proc Natl Acad Sci U S A 123: e2528400123-e2528400123

PubMed: 42085157 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2528400123
Primary Citation Related Structures:
9DO6, 9DO7, 9DO8, 9DO9, 9DOA, 9DOB

PubMed Abstract:
Biomembranes are complex two-dimensional liquids composed of hundreds of lipid species that interact in a myriad of ways. One such interaction, that between sphingomyelin (SM) and cholesterol in plasma membranes of animal cells, provides many functional benefits, including protection from microbial infection, prevention of unrestrained cell growth, and proper maintenance of cellular lipid composition. Owing to the liquid nature of membranes, the structure of the SM/cholesterol interaction, or any other functionally critical lipid-lipid interaction, has remained elusive. Here, we overcome this challenge using a fungal toxin called Ostreolysin A (OlyA), that has been shown to specifically bind to SM/cholesterol complexes in membranes. We used OlyA to stabilize the SM/cholesterol interaction much in the same way as antibodies are used to stabilize preexisting protein complexes. Cryoelectron microscopy analysis of OlyA bound to SM/cholesterol membranes reveals the details of the tight interaction between these two lipids-the steroid nucleus of cholesterol packs against the acyl chains of SM, and a hydrogen bond forms between the nitrogen on SM's ceramide base and the oxygen on cholesterol's hydroxyl group, thus sequestering this key functional group of cholesterol. The importance of hydrogen bonding in stabilizing the SM/cholesterol interaction is supported by structural analysis of a mutant form of OlyA that binds free SM in a cholesterol-independent manner. These results provide structural insights into the organization of cholesterol in membranes.

Organizational Affiliation

Department of Molecular Genetics, University of Texas, Southwestern Medical Center, Dallas, TX 75390-9046.

Macromolecule Content

Total Structure Weight: 181.14 kDa
Atom Count: 11,884
Modeled Residue Count: 1,432
Deposited Residue Count: 1,538
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ostreolysin A6	A, B, D [auth L], E [auth M]	143	Pleurotus ostreatus	Mutation(s): 1 Gene Names: OlyA6
UniProt
Find proteins for P83467 (Pleurotus ostreatus) Explore P83467 Go to UniProtKB: P83467
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P83467
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pleurotolysin B	C, F [auth N]	483	Pleurotus ostreatus	Mutation(s): 0 Gene Names: plyB
UniProt
Find proteins for Q5W9E8 (Pleurotus ostreatus) Explore Q5W9E8 Go to UniProtKB: Q5W9E8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5W9E8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A8R (Subject of Investigation/LOI) Query on A1A8R Download:Ideal Coordinates CCD File SDF format, chain V [auth M] SDF format, chain U [auth M] SDF format, chain T [auth M] SDF format, chain S [auth M] SDF format, chain R [auth L] SDF format, chain Q [auth L] SDF format, chain P [auth L] SDF format, chain O [auth L] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain V [auth M] MOL2 format, chain U [auth M] MOL2 format, chain T [auth M] MOL2 format, chain S [auth M] MOL2 format, chain R [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain P [auth L] MOL2 format, chain O [auth L] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain V [auth M] mmCIF format, chain U [auth M] mmCIF format, chain T [auth M] mmCIF format, chain S [auth M] mmCIF format, chain R [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain P [auth L] mmCIF format, chain O [auth L] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth B] G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth L], P [auth L], Q [auth L], R [auth L], S [auth M], T [auth M], U [auth M], V [auth M]	N-oleoyl-D-erythro-sphingosylphosphorylcholine C₄₁ H₈₂ N₂ O₆ P NBEADXWAAWCCDG-QDDWGVBQSA-O		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain V [auth M] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain V [auth M]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL160487
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI158357
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM131963
Welch Foundation	United States	I-1793
Leducq Foundation	France	19CVD04