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- PDB-9ign: Aerolysin E254A/E258A in styrene-maleic acid lipid particles -

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Basic information

Entry
Database: PDB / ID: 9ign
TitleAerolysin E254A/E258A in styrene-maleic acid lipid particles
ComponentsAerolysin
KeywordsTOXIN / Pore forming toxin Styrene maleic acid lipid particle
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Aerolysin / : / Aerolysin toxin / Aerolysin toxin / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / C-type lectin fold
Similarity search - Domain/homology
Biological speciesAeromonas hydrophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsAnton, J.S. / Bada Juarez, J.F. / Marcaida, M.J. / Dal Peraro, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation200021L_212128 Switzerland
CitationJournal: Nat Nanotechnol / Year: 2025
Title: Lumen charge governs gated ion transport in β-barrel nanopores.
Authors: Simon Finn Mayer / Marianna Fanouria Mitsioni / Paul Robin / Lukas van den Heuvel / Nathan Ronceray / Maria Jose Marcaida / Luciano A Abriata / Lucien F Krapp / Jana S Anton / Sarah Soussou ...Authors: Simon Finn Mayer / Marianna Fanouria Mitsioni / Paul Robin / Lukas van den Heuvel / Nathan Ronceray / Maria Jose Marcaida / Luciano A Abriata / Lucien F Krapp / Jana S Anton / Sarah Soussou / Justin Jeanneret-Grosjean / Alessandro Fulciniti / Alexia Möller / Sarah Vacle / Lely Feletti / Henry Brinkerhoff / Andrew H Laszlo / Jens H Gundlach / Theo Emmerich / Matteo Dal Peraro / Aleksandra Radenovic /
Abstract: β-Barrel nanopores are involved in crucial biological processes, from ATP export in mitochondria to bacterial resistance, and represent a promising platform for emerging sequencing technologies. ...β-Barrel nanopores are involved in crucial biological processes, from ATP export in mitochondria to bacterial resistance, and represent a promising platform for emerging sequencing technologies. However, in contrast to ion channels, the understanding of the fundamental principles governing ion transport through these nanopores remains largely unexplored. Here we integrate experimental, numerical and theoretical approaches to elucidate ion transport mechanisms in β-barrel nanopores. We identify and characterize two distinct nonlinear phenomena: open-pore rectification and gating. Through extensive mutation analysis of aerolysin nanopores, we demonstrate that open-pore rectification is caused by ionic accumulation driven by the distribution of lumen charges. In addition, we provide converging evidence suggesting that gating is controlled by electric fields dissociating counterions from lumen charges, promoting local structural deformations. Our findings establish a rigorous framework for characterizing and understanding ion transport processes in protein-based nanopores, enabling the design of adaptable nanofluidic biotechnologies. We illustrate this by optimizing an aerolysin mutant for computing applications.
History
DepositionFeb 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aerolysin
B: Aerolysin
C: Aerolysin
D: Aerolysin
E: Aerolysin
F: Aerolysin
G: Aerolysin
H: Aerolysin
I: Aerolysin
J: Aerolysin
K: Aerolysin
L: Aerolysin
M: Aerolysin
N: Aerolysin


Theoretical massNumber of molelcules
Total (without water)658,96714
Polymers658,96714
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Aerolysin


Mass: 47069.086 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: aerA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09167
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Aerolysin E254A/E258A / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Aeromonas hydrophila (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115756 / Symmetry type: POINT
RefinementHighest resolution: 2.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00540285
ELECTRON MICROSCOPYf_angle_d0.70555020
ELECTRON MICROSCOPYf_dihedral_angle_d12.97714217
ELECTRON MICROSCOPYf_chiral_restr0.0515663
ELECTRON MICROSCOPYf_plane_restr0.0067203

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