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- EMDB-52853: Aerolysin E254A/E258A in styrene-maleic acid lipid particles -

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Basic information

Entry
Database: EMDB / ID: EMD-52853
TitleAerolysin E254A/E258A in styrene-maleic acid lipid particles
Map data
Sample
  • Complex: Aerolysin E254A/E258A
    • Protein or peptide: Aerolysin
KeywordsPore forming toxin Styrene maleic acid lipid particle / TOXIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsAnton JS / Bada Juarez JF / Marcaida MJ / Dal Peraro M
Funding support Switzerland, 1 items
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, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52853.png

Downloads & links

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Map

FileDownload / File: emd_52853.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 440 pix.
= 289.52 Å		0.66 Å/pix.
x 440 pix.
= 289.52 Å		0.66 Å/pix.
x 440 pix.
= 289.52 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.1909087 - 0.42264768
Average (Standard dev.)0.00021579815 (±0.01746416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 289.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52853_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_52853_half_map_2.map
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Sample components

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Entire : Aerolysin E254A/E258A

EntireName: Aerolysin E254A/E258A
Components
  • Complex: Aerolysin E254A/E258A
    • Protein or peptide: Aerolysin

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Supramolecule #1: Aerolysin E254A/E258A

SupramoleculeName: Aerolysin E254A/E258A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aeromonas hydrophila (bacteria)

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Macromolecule #1: Aerolysin

MacromoleculeName: Aerolysin / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Aeromonas hydrophila (bacteria)
Molecular weightTheoretical: 47.069086 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AEPVYPDQLR LFSLGQGVCG DKYRPVNREE AQSVKSNIVG MMGQWQISGL ANGWVIMGPG YNGEIKPGTA SNTWCYPTNP VTGEIPTLS ALDIPDGDEV DVQWRLVHDS ANFIKPTSYL AHYLGYAWVG GNHSQYVGED MDVTRDGDGW VIRGNNDGGC D GYRCGDKT ...String:
AEPVYPDQLR LFSLGQGVCG DKYRPVNREE AQSVKSNIVG MMGQWQISGL ANGWVIMGPG YNGEIKPGTA SNTWCYPTNP VTGEIPTLS ALDIPDGDEV DVQWRLVHDS ANFIKPTSYL AHYLGYAWVG GNHSQYVGED MDVTRDGDGW VIRGNNDGGC D GYRCGDKT AIKVSNFAYN LDPDSFKHGD VTQSDRQLVK TVVGWAVNDS DTPQSGYDVT LRYDTATNWS KTNTYGLSEK VT TKNKFKW PLVGETALSI AIAANQSWAS QNGGSTTTSL SQSVRPTVPA RSKIPVKIEL YKADISYPYE FKADVSYDLT LSG FLRWGG NAWYTHPDNR PNWNHTFVIG PYKDKASSIR YQWDKRYIPG EVKWWDWNWT IQQNGLSTMQ NNLARVLRPV RAGI TGDFS AESQFAGNIE IGAPVPLAA

UniProtKB: Aerolysin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 115756
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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