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 1.0 of the entry. See complete history.

Literature

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

Smothers, J., Chen, Z., Li, Y., Han, Y., Radhakrishnan, A.

To be published.

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

View Full Validation Report

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

Revision History (Full details and data files)

Version 1.0: 2025-09-24
Type: Initial release

9DOB | pdb_00009dob

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

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2