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- EMDB-63781: Cryo-EM structure of alpha-hemolysin heptameric pre-pore state II... -

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Basic information

Entry
Database: EMDB / ID: EMD-63781
TitleCryo-EM structure of alpha-hemolysin heptameric pre-pore state III in the presence of RBC
Map dataAlpha-hemolysin heptameric pre-pore state III derived from RBC
Sample
  • Complex: heptamer of alpha-hemolysin
    • Protein or peptide: Alpha-hemolysin
Keywordssmall PFT / RBC / pre-pore / TOXIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChatterjee A / Roy A / Dutta S
Funding support India, 1 items
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, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63781.png

Downloads & links

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Map

FileDownload / File: emd_63781.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAlpha-hemolysin heptameric pre-pore state III derived from RBC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 280 pix.
= 257.6 Å		0.92 Å/pix.
x 280 pix.
= 257.6 Å		0.92 Å/pix.
x 280 pix.
= 257.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0515
Minimum - Maximum-0.28235435 - 0.43748987
Average (Standard dev.)0.00044354904 (±0.012559649)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 257.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map of alpha-hemolysin heptameric pre-pore state III derived...

Fileemd_63781_half_map_1.map
AnnotationHalf-map of alpha-hemolysin heptameric pre-pore state III derived from RBC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of alpha-hemolysin heptameric pre-pore state III derived...

Fileemd_63781_half_map_2.map
AnnotationHalf-map of alpha-hemolysin heptameric pre-pore state III derived from RBC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : heptamer of alpha-hemolysin

EntireName: heptamer of alpha-hemolysin
Components
  • Complex: heptamer of alpha-hemolysin
    • Protein or peptide: Alpha-hemolysin

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Supramolecule #1: heptamer of alpha-hemolysin

SupramoleculeName: heptamer of alpha-hemolysin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylococcus aureus (bacteria)

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Macromolecule #1: Alpha-hemolysin

MacromoleculeName: Alpha-hemolysin / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 33.29 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ADSDINIKTG TTDIGSNTTV KTGDLVTYDK ENGMHKKVFY SFIDDKNHNK KLLVIRTKGT IAGQYRVYSE EGANKSGLAW PSAFKVQLQ LPDNEVAQIS DYYPRNSIDT KEYMSTLTYG FNGNVTGDDT GKIGGLIGAN VSIGHTLKYV QPDFKTILES P TDKKVGWK ...String:
ADSDINIKTG TTDIGSNTTV KTGDLVTYDK ENGMHKKVFY SFIDDKNHNK KLLVIRTKGT IAGQYRVYSE EGANKSGLAW PSAFKVQLQ LPDNEVAQIS DYYPRNSIDT KEYMSTLTYG FNGNVTGDDT GKIGGLIGAN VSIGHTLKYV QPDFKTILES P TDKKVGWK VIFNNMVNQN WGPYDRDSWN PVYGNQLFMK TRNGSMKAAD NFLDPNKASS LLSSGFSPDF ATVITMDRKA SK QQTNIDV IYERVRDDYQ LHWTSTNWKG TNTKDKWTDR SSERYKIDWE KEEMTN

UniProtKB: Alpha-hemolysin

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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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50694
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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