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- PDB-9mbx: Cryo-EM structure of alpha-hemolysin heptameric pre-pore state II... -

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Basic information

Entry
Database: PDB / ID: 9mbx
TitleCryo-EM structure of alpha-hemolysin heptameric pre-pore state III in the presence of RBC
ComponentsAlpha-hemolysin
KeywordsTOXIN / small PFT / RBC / pre-pore
Function / homology
Function and homology information


cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChatterjee, A. / Roy, A. / Dutta, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
CitationJournal: J Cell Biol / Year: 2026
Title: Stepwise assembly of α-hemolysin from intermediates to the mature pore in native erythrocytes.
Authors: Arnab Chatterjee / Anupam Roy / Partho Pratim Das / Debajyoti Chakraborty / Bartika Ghoshal / Siddharth Jhunjhunwala / Somnath Dutta /
Abstract: Alpha-hemolysin (α-HL) is a small pore-forming toxin secreted by pathogenic Staphylococcus aureus, inducing cell death process by forming pores in membrane. So far, detergents or artificial lipid ...Alpha-hemolysin (α-HL) is a small pore-forming toxin secreted by pathogenic Staphylococcus aureus, inducing cell death process by forming pores in membrane. So far, detergents or artificial lipid environments have been utilized to characterize the toxin structure. The toxin-induced changes in the membrane, membrane remodeling after toxin treatment, and the role of the toxin during pore formation process remain ambiguous. Thus, understanding pore formation in the cellular environment, including the roles of the plasma membrane and lipid composition, is crucial for drug development. In this study, we captured step-by-step oligomerization of α-HL and membrane rupture of erythrocyte cells using confocal microscopy, cryo-EM imaging, and single-particle analysis. We resolved 3.1-3.8 Å resolution structures of pore, prepore, and immature pore conformations in cellular environment. Furthermore, mass spectrometry analysis demonstrated key erythrocyte lipid components interacting with α-HL. Our findings indicate that shorter or unsaturated lipid chains facilitate pore formation and the role of phosphatidylcholine with varying physical properties in modulating the toxin's activity.
History
DepositionMar 17, 2025Deposition site: PDBJ / Processing site: PDBJ
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
F: Alpha-hemolysin
A: Alpha-hemolysin
B: Alpha-hemolysin
C: Alpha-hemolysin
D: Alpha-hemolysin
E: Alpha-hemolysin
G: Alpha-hemolysin


Theoretical massNumber of molelcules
Total (without water)233,0307
Polymers233,0307
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Alpha-hemolysin / Alpha-HL / Alpha-toxin


Mass: 33290.000 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hly, hla / Production host: Escherichia coli (E. coli) / References: UniProt: P09616
Has protein modificationN

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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: heptamer of alpha-hemolysin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50694 / Symmetry type: POINT
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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