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- EMDB-50059: The structure of solubilized octameric pore of actinoporin Fav pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-50059
TitleThe structure of solubilized octameric pore of actinoporin Fav prepared on POPG, cholesterol, sphingomyelin membranes
Map datamain map
Sample
  • Complex: Octameric Fav pore in complex with sphingomyelin and cholesterol molecules solubilized by detergents
    • Protein or peptide: Actinoporin
  • Ligand: CHOLESTEROL
  • Ligand: Sphingomyelin C18
KeywordsActinoporin / Pore-forming toxin / Pore / Octamer / Transmembrane pore / TOXIN / cholesterol / nanopore
Biological speciesOrbicella faveolata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsSolinc G / Srnko M / Anderluh G / Podobnik M
Funding support Slovenia, 3 items
OrganizationGrant numberCountry
Slovenian Research AgencyJ4-8225 Slovenia
Slovenian Research AgencyP1-0391 Slovenia
Other private
CitationJournal: To Be Published
Title: The structure of solubilized octameric pore of actinoporin Fav prepared on DOPC:sphingomyelin membranes
Authors: Solinc G / Srnko M / Anderluh G / Podobnik M
History
DepositionApr 9, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50059.png

Downloads & links

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Map

FileDownload / File: emd_50059.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 320 pix.
= 302.624 Å		0.95 Å/pix.
x 320 pix.
= 302.624 Å		0.95 Å/pix.
x 320 pix.
= 302.624 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9457 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.91
Minimum - Maximum-6.3060284 - 8.277505
Average (Standard dev.)-0.0016093034 (±0.20489873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 302.624 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_50059_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_50059_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Octameric Fav pore in complex with sphingomyelin and cholesterol ...

EntireName: Octameric Fav pore in complex with sphingomyelin and cholesterol molecules solubilized by detergents
Components
  • Complex: Octameric Fav pore in complex with sphingomyelin and cholesterol molecules solubilized by detergents
    • Protein or peptide: Actinoporin
  • Ligand: CHOLESTEROL
  • Ligand: Sphingomyelin C18

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Supramolecule #1: Octameric Fav pore in complex with sphingomyelin and cholesterol ...

SupramoleculeName: Octameric Fav pore in complex with sphingomyelin and cholesterol molecules solubilized by detergents
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Details: Octameric Fav pore prepared on 1-Palmitoyl-2-oleoyl-sn-glycero-3-(phospho-rac-(1-glycerol)) (POPG):sphingomyelin:cholesterol (1:1:1 molar ratio) membranes
Source (natural)Organism: Orbicella faveolata (invertebrata)

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Macromolecule #1: Actinoporin

MacromoleculeName: Actinoporin / type: protein_or_peptide / ID: 1
Details: This protein was expressed with an N-terminal addition of 6xHis tag and TEV cleavage site. After removing the His-tag, the final construct has three additional residues at the N-terminal (GHM).
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Orbicella faveolata (invertebrata)
Molecular weightTheoretical: 23.002561 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GHMHNAEAIP QEPMDLENLD SEKRAARIAA GTIIAGAELT IGLLQNLLDV LANVNRKCAV GVDNESGFRW QEGSTYFFSG TADENLPYS VSDGYAVLYG PRKTNGPVAT GVVGVLAYYI PSIGKTLAVM WSVPFDYNFY QNWWNAKLYS GNQDADYDHY V DLYYDANP ...String:
GHMHNAEAIP QEPMDLENLD SEKRAARIAA GTIIAGAELT IGLLQNLLDV LANVNRKCAV GVDNESGFRW QEGSTYFFSG TADENLPYS VSDGYAVLYG PRKTNGPVAT GVVGVLAYYI PSIGKTLAVM WSVPFDYNFY QNWWNAKLYS GNQDADYDHY V DLYYDANP FKANGWHERS LGSGLKFCGS MSSSGQATLE IHVLKESETC M

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 32 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: Sphingomyelin C18

MacromoleculeName: Sphingomyelin C18 / type: ligand / ID: 3 / Number of copies: 88 / Formula: A1H8M
Molecular weightTheoretical: 732.089 Da

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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

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris
0.02 %Brij 35

Details: 150 mM NaCl, 50 mM Tris/HCl, 0.02 % Brij 35, pH 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 11470 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 2705265 / Details: Number of particles after template picking
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C8 (8 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 118851
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: Pore structure of the same protein from related entries
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9eyo:
The structure of solubilized octameric pore of actinoporin Fav prepared on POPG, cholesterol, sphingomyelin membranes

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