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

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9gxj
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: To Be Published
Title: Lumen charge governs rectification and gating in beta-barrel nanopores
Authors: Mayer, S.F. / Mitsioni, M.F. / van den Heuvel, L. / Robin, P. / Ronceray, N. / Marcaida, M.J. / Abriata, L.A. / Krapp, L.F. / Anton, J.S. / Soussou, S. / Jeanneret-Grosjean, J. / Fulciniti, ...Authors: Mayer, S.F. / Mitsioni, M.F. / van den Heuvel, L. / Robin, P. / Ronceray, N. / Marcaida, M.J. / Abriata, L.A. / Krapp, L.F. / Anton, J.S. / Soussou, S. / Jeanneret-Grosjean, J. / Fulciniti, A. / Moeller, A. / Vacle, S. / Feletti, L. / Brinkerhoff, H. / Laszlo, A.H. / Gundlach, J.H. / Emmerich, T. / Dal Peraro, M. / Radenovic, A.
History
DepositionSep 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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


Theoretical massNumber of molelcules
Total (without water)329,4847
Polymers329,4847
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.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: aerA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (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 softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95488 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00422995
ELECTRON MICROSCOPYf_angle_d0.60531388
ELECTRON MICROSCOPYf_dihedral_angle_d11.1488148
ELECTRON MICROSCOPYf_chiral_restr0.0473297
ELECTRON MICROSCOPYf_plane_restr0.0044088

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