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- EMDB-62310: Alpha-hemolysin heptameric pore state derived from 10:0 PC liposomes -

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Basic information

Entry
Database: EMDB / ID: EMD-62310
TitleAlpha-hemolysin heptameric pore state derived from 10:0 PC liposomes
Map dataAlpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes (Mask refined map)
Sample
  • Complex: heptamer of alpha-hemolysin
    • Protein or peptide: Alpha-hemolysin
KeywordsPFT / Liposomes / LIPID BINDING PROTEIN
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: 2.8 Å
AuthorsChatterjee A / Roy A / Dutta S
Funding support India, 1 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) 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_62310.png

Downloads & links

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Map

FileDownload / File: emd_62310.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAlpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes (Mask refined map)
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: 0.0845
Minimum - Maximum-0.60259676 - 0.83408254
Average (Standard dev.)0.000607929 (±0.03414511)
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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Additional map: Alpha-hemolysin heptameric pore state derived from egg PC/Cholesterol...

Fileemd_62310_additional_1.map
AnnotationAlpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio) 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_62310_half_map_1.map
AnnotationHalf-map of alpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes (Mask refined map)
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_62310_half_map_2.map
AnnotationHalf-map of alpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes (Mask refined 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 : 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127106
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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