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- EMDB-50057: The structure of solubilized octameric pore of actinoporin Fav pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-50057
TitleThe structure of solubilized octameric pore of actinoporin Fav prepared on DOPC:sphingomyelin membranes
Map dataMain map
Sample
  • Complex: Octameric Fav pore in complex with sphingomyelin molecules solubilized by detergents
    • Protein or peptide: Actinoporin
  • Ligand: Sphingomyelin C18
KeywordsActinoporin / Pore-forming toxin / Pore / Octamer / Transmembrane pore / TOXIN / Nanopore
Biological speciesOrbicella faveolata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSolinc G / Srnko M / Svigel T / 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 / Svigel T / 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_50057.png

Downloads & links

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Map

FileDownload / File: emd_50057.map.gz / Format: CCP4 / Size: 64 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.)
1.04 Å/pix.
x 256 pix.
= 267.008 Å		1.04 Å/pix.
x 256 pix.
= 267.008 Å		1.04 Å/pix.
x 256 pix.
= 267.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.043 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.542
Minimum - Maximum-2.368847 - 4.1156693
Average (Standard dev.)0.006241412 (±0.11804943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 267.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map used for building the transmembrane region

Fileemd_50057_additional_1.map
AnnotationSharpened map used for building the transmembrane region
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_50057_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_50057_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 molecules solubi...

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

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Supramolecule #1: Octameric Fav pore in complex with sphingomyelin molecules solubi...

SupramoleculeName: Octameric Fav pore in complex with sphingomyelin molecules solubilized by detergents
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Octameric Fav pore prepared on 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC):sphingomyelin (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: 28.80326 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GHMSAPIKAN DPNGEVLEEM PKTKRGAEAL LADVGLAHFP EMVPNRQELR ALLKRSHNAE AIPQEPMDLE NLDSEKRAAR IAAGTIIAG AELTIGLLQN LLDVLANVNR KCAVGVDNES GFRWQEGSTY FFSGTADENL PYSVSDGYAV LYGPRKTNGP V ATGVVGVL ...String:
GHMSAPIKAN DPNGEVLEEM PKTKRGAEAL LADVGLAHFP EMVPNRQELR ALLKRSHNAE AIPQEPMDLE NLDSEKRAAR IAAGTIIAG AELTIGLLQN LLDVLANVNR KCAVGVDNES GFRWQEGSTY FFSGTADENL PYSVSDGYAV LYGPRKTNGP V ATGVVGVL AYYIPSIGKT LAVMWSVPFD YNFYQNWWNA KLYSGNQDAD YDHYVDLYYD ANPFKANGWH ERSLGSGLKF CG SMSSSGQ ATLEIHVLKE SETCM

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Macromolecule #2: Sphingomyelin C18

MacromoleculeName: Sphingomyelin C18 / type: ligand / ID: 2 / Number of copies: 48 / 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

Concentration5 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 R2/2 / 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: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 2073 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 802336
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C8 (8 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4) / Number images used: 174291
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9eym:
The structure of solubilized octameric pore of actinoporin Fav prepared on DOPC:sphingomyelin membranes

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