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- EMDB-62302: Cryo-EM Density map of Staphylococcus aureus alpha-hemolysin pore... -

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Entry
Database: EMDB / ID: EMD-62302
TitleCryo-EM Density map of Staphylococcus aureus alpha-hemolysin pore structure derived from 12:0 Phosphatidylcholine (12:0 PC) liposome
Map dataMap of Alpha-hemolysin heptameric pore state derived from 12:0 PC liposomes
Sample
  • Complex: Heptameric complex of alpha-hemolysin pore species of Staphylococcus aureus derived from 12:0 Phosphatidylcholine (12:0 PC) liposome
KeywordsPore-forming toxin / Alpha hemolysin / 12:0 Phosphatidylcholine liposome / Pore / TOXIN
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsChatterjee A / Dutta S / Roy A
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)(BT/INF/22/SP22844/2017) India
Department of Science & Technology (DST, India)SR/FST/LSII-039/2015 India
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into pre-pore intermediates of alpha-hemolysin in the lipidic environment.
Authors: Arnab Chatterjee / Anupam Roy / Thejas Satheesh / Partho Pratim Das / Bapan Mondal / Prithiv Kishore / Mahipal Ganji / Somnath Dutta /
Abstract: The infectious microbe Staphylococcus aureus releases an array of cytotoxic pore-forming toxins (PFTs) that severely damage the cell membrane during bacterial infection. However, the interaction ...The infectious microbe Staphylococcus aureus releases an array of cytotoxic pore-forming toxins (PFTs) that severely damage the cell membrane during bacterial infection. However, the interaction interfaces between the host cell membrane and toxin were hardly explored. So far, there are no pore, and intermediate structures of these toxins available in the presence of bio-membrane, which could elucidate the pore-forming mechanism. Here, we investigate the structure of different conformational states of this alpha-hemolysin (α-HL/Hla), a β-PFT in lipidic environment using single-particle cryo-EM. Additionally, we explore lipid destabilization by the toxin, using single-molecule imaging, confocal imaging, and validation of lipid-protein interactions using mutational studies. We elucidate eight cryo-EM structures of wildtype α-HL with various liposomes, which are composed of either 10:0 PC or Egg-PC/Cholesterol or Egg-PC/Sphingomyelin or 10:0 PC/Sphingomyelin. Our structural and biophysical studies confirm that different chain lengths and various membrane compositions facilitate the formation of intermediate pre-pores and complete pore species. We also demonstrate that the percentage of pre-pore population increases due to sphingomyelin-induced membrane rigidity. Altogether, this study unveils the structure-function analysis of the pre-pore to pore transition of wildtype α-HL during its crosstalk with the lipid membrane.
History
DepositionNov 7, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62302.png

Downloads & links

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Map

FileDownload / File: emd_62302.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of Alpha-hemolysin heptameric pore state derived from 12:0 PC liposomes
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: 0.09
Minimum - Maximum-0.64949685 - 0.9403826
Average (Standard dev.)0.0003463409 (±0.025699958)
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 pore state derived from...

Fileemd_62302_half_map_1.map
AnnotationHalf-map of Alpha-hemolysin heptameric pore state derived from 12:0 PC liposomes
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 pore state derived from...

Fileemd_62302_half_map_2.map
AnnotationHalf-map of Alpha-hemolysin heptameric pore state derived from 12:0 PC liposomes
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Heptameric complex of alpha-hemolysin pore species of Staphylococ...

EntireName: Heptameric complex of alpha-hemolysin pore species of Staphylococcus aureus derived from 12:0 Phosphatidylcholine (12:0 PC) liposome
Components
  • Complex: Heptameric complex of alpha-hemolysin pore species of Staphylococcus aureus derived from 12:0 Phosphatidylcholine (12:0 PC) liposome

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Supramolecule #1: Heptameric complex of alpha-hemolysin pore species of Staphylococ...

SupramoleculeName: Heptameric complex of alpha-hemolysin pore species of Staphylococcus aureus derived from 12:0 Phosphatidylcholine (12:0 PC) liposome
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Staphylococcus aureus (bacteria)
Molecular weightTheoretical: 330 KDa

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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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94339
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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