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- EMDB-50578: aerolysin WT pore in LMNG:CHS -

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Basic information

Entry
Database: EMDB / ID: EMD-50578
Titleaerolysin WT pore in LMNG:CHS
Map datapostprocessed map WT aerolysin in LMNG:CHS
Sample
  • Complex: aerolysin pore
    • Protein or peptide: aerolysin
Keywordspore forming toxin / aerolysin / cryo-EM / TOXIN
Biological speciesAeromonas hydrophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsZuber B / Ioan I
Funding support Switzerland, 3 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179520 Switzerland
Swiss National Science Foundation32NE30_185536 Switzerland
Swiss National Science Foundation222809 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 7, 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_50578.png

Downloads & links

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Map

FileDownload / File: emd_50578.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocessed map WT aerolysin in LMNG:CHS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å		0.73 Å/pix.
x 400 pix.
= 292. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.048293762 - 0.076200075
Average (Standard dev.)0.000048212834 (±0.0018508352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 292.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: aerolysin WT map in LMNG:CHS

Fileemd_50578_additional_1.map
Annotationaerolysin WT map in LMNG:CHS
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50578_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50578_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : aerolysin pore

EntireName: aerolysin pore
Components
  • Complex: aerolysin pore
    • Protein or peptide: aerolysin

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Supramolecule #1: aerolysin pore

SupramoleculeName: aerolysin pore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: oligomer generated by proteolytic activation of aerolysin in presence of LMNG:CHS
Source (natural)Organism: Aeromonas hydrophila (bacteria)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: aerolysin

MacromoleculeName: aerolysin / type: protein_or_peptide / ID: 1
Details: sample was cleaved with trypsin prior to oligomerization removing the C-terminus and Hisx6 tag.
Enantiomer: LEVO
Source (natural)Organism: Aeromonas hydrophila (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AEPVYPDQLR LFSLGQGVCG DKYRPVNREE AQSVKSNIVG MMGQWQISGL ANGWVIMGPG YNGEIKPGTA SNTWCYPTNP VTGEIPTLSA LDIPDGDEVD VQWRLVHDSA NFIKPTSYLA HYLGYAWVGG NHSQYVGEDM DVTRDGDGWV IRGNNDGGCD GYRCGDKTAI ...String:
AEPVYPDQLR LFSLGQGVCG DKYRPVNREE AQSVKSNIVG MMGQWQISGL ANGWVIMGPG YNGEIKPGTA SNTWCYPTNP VTGEIPTLSA LDIPDGDEVD VQWRLVHDSA NFIKPTSYLA HYLGYAWVGG NHSQYVGEDM DVTRDGDGWV IRGNNDGGCD GYRCGDKTAI KVSNFAYNLD PDSFKHGDVT QSDRQLVKTV VGWAVNDSDT PQSGYDVTLR YDTATNWSKT NTYGLSEKVT TKNKFKWPLV GETELSIEIA ANQSWASQNG GSTTTSLSQS VRPTVPARSK IPVKIELYKA DISYPYEFKA DVSYDLTLSG FLRWGGNAWY THPDNRPNWN HTFVIGPYKD KASSIRYQWD KRYIPGEVKW WDWNWTIQQN GLSTMQNNLA RVLRPVRAGI TGDFSAESQF AGNIEIGAPV PLAADSKVRR ARSVDGAGQG LRLEIPLDAQ ELSGLGFNNV SLSVTPAANQ LEHHHHHH

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133420
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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