9DO9 | pdb_00009do9

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

PDB DOI: https://doi.org/10.2210/pdb9DO9/pdb
EM Map EMD-47076: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Pleurotus ostreatus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

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: 2.91 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/PlyB (Hinge-Lock) prepore focused refinement

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

To be published.

Macromolecule Content

Total Structure Weight: 181.55 kDa
Atom Count: 11,924
Modeled Residue Count: 1,432
Deposited Residue Count: 1,538
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ostreolysin A6	A, B, D [auth N], E [auth O]	143	Pleurotus ostreatus	Mutation(s): 0 Gene Names: OlyA6
UniProt
Find proteins for P83467 (Pleurotus ostreatus) Explore P83467 Go to UniProtKB: P83467
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P83467
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pleurotolysin B	C, F [auth P]	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5W9E8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 X [auth O] SDF format, chain W [auth O] SDF format, chain V [auth O] SDF format, chain S [auth N] SDF format, chain R [auth N] SDF format, chain Q [auth N] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain X [auth O] MOL2 format, chain W [auth O] MOL2 format, chain V [auth O] MOL2 format, chain S [auth N] MOL2 format, chain R [auth N] MOL2 format, chain Q [auth N] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain X [auth O] mmCIF format, chain W [auth O] mmCIF format, chain V [auth O] mmCIF format, chain S [auth N] mmCIF format, chain R [auth N] mmCIF format, chain Q [auth N] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] 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] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], Q [auth N], R [auth N], S [auth N], V [auth O], W [auth O], X [auth O]	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 L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth N] Focus chain R [auth N] Focus chain S [auth N] Focus chain V [auth O] Focus chain W [auth O] Focus chain X [auth O] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth N] Focus chain R [auth N] Focus chain S [auth N] Focus chain V [auth O] Focus chain W [auth O] Focus chain X [auth O]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain Z [auth O] SDF format, chain Y [auth O] SDF format, chain U [auth N] SDF format, chain T [auth N] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain Z [auth O] MOL2 format, chain Y [auth O] MOL2 format, chain U [auth N] MOL2 format, chain T [auth N] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain Z [auth O] mmCIF format, chain Y [auth O] mmCIF format, chain U [auth N] mmCIF format, chain T [auth N] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A] K [auth A] O [auth B] P [auth B] T [auth N] J [auth A], K [auth A], O [auth B], P [auth B], T [auth N], U [auth N], Y [auth O], Z [auth O]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth N] Focus chain U [auth N] Focus chain Y [auth O] Focus chain Z [auth O] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth N] Focus chain U [auth N] Focus chain Y [auth O] Focus chain Z [auth O]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.91 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

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