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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: To Be Published
Title: Alpha-hemolysin heptameric pore state derived from 10:0 PC liposomes
Authors: Chatterjee A / Roy A / Dutta S
History
DepositionNov 7, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 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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