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- EMDB-50549: Aerolysin Wildtype in styrene-maleic acid lipid particles -

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Basic information

Entry
Database: EMDB / ID: EMD-50549
TitleAerolysin Wildtype in styrene-maleic acid lipid particles
Map data
Sample
  • Complex: Aerolysin
    • Protein or peptide: Aerolysin
KeywordsPore forming toxin Styrene maleic acid lipid particle / TOXIN
Function / homology
Function and homology information


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: 2.2 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: J Am Chem Soc / Year: 2025
Title: Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment.
Authors: Jana S Anton / Ioan Iacovache / Juan F Bada Juarez / Luciano A Abriata / Louis W Perrin / Chan Cao / Maria J Marcaida / Benoît Zuber / Matteo Dal Peraro /
Abstract: Aerolysin is a β-pore-forming toxin produced by most Aeromonas bacteria, which has attracted large attention in the field of nanopore sensing due to its narrow and charged pore lumen. Structurally ...Aerolysin is a β-pore-forming toxin produced by most Aeromonas bacteria, which has attracted large attention in the field of nanopore sensing due to its narrow and charged pore lumen. Structurally similar proteins, belonging to the aerolysin-like family, are present throughout all kingdoms of life, but very few of them have been structurally characterized in a lipid environment. Here, we present the first high-resolution atomic cryo-EM structures of aerolysin prepore and pore in a membrane-like environment. These structures allow the identification of key interactions, which are relevant for understanding the pore formation mechanism and for correctly positioning the pore β-barrel and its anchoring β-turn motif in the membrane. Moreover, we elucidate at high resolution the architecture of key pore mutations and precisely identify four constriction rings in the pore lumen that are highly relevant for nanopore sensing experiments.
History
DepositionJun 5, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50549.png

Downloads & links

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Map

FileDownload / File: emd_50549.map.gz / Format: CCP4 / Size: 216 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.)
0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.174
Minimum - Maximum-1.4276302 - 2.3176591
Average (Standard dev.)-0.000012221832 (±0.067785904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50549_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_50549_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Aerolysin

EntireName: Aerolysin
Components
  • Complex: Aerolysin
    • Protein or peptide: Aerolysin

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Supramolecule #1: Aerolysin

SupramoleculeName: Aerolysin / 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: 7 / Enantiomer: LEVO
Source (natural)Organism: Aeromonas hydrophila (bacteria)
Molecular weightTheoretical: 47.185152 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 PLVGETELSI EIAANQSWAS 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 89384
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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