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- EMDB-50061: The structure of octameric pore of RN1 variant of actinoporin Fav -

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Basic information

Entry
Database: EMDB / ID: EMD-50061
TitleThe structure of octameric pore of RN1 variant of actinoporin Fav
Map dataMain map
Sample
  • Complex: Octameric RN1-Fav pore
    • Protein or peptide: Actinoporin
  • Ligand: Sphingomyelin C18
KeywordsActinoporin / Pore-forming toxin / Pore / Octamer / Transmembrane pore / TOXIN / Protein nanopore
Biological speciesOrbicella faveolata (invertebrata)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsSolinc G / Srnko M / Anderluh G / Crnkovic A / 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 octameric pore of RN1 variant of actinoporin Fav
Authors: Solinc G / Srnko M / Anderluh G / Podobnik M / Crnkovic A
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_50061.png

Downloads & links

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Map

FileDownload / File: emd_50061.map.gz / Format: CCP4 / Size: 307.5 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.)
0.75 Å/pix.
x 432 pix.
= 321.84 Å		0.75 Å/pix.
x 432 pix.
= 321.84 Å		0.75 Å/pix.
x 432 pix.
= 321.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.745 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.665
Minimum - Maximum-5.3075933 - 7.9085593
Average (Standard dev.)-0.0021040149 (±0.14778009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 321.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_50061_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_50061_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 RN1-Fav pore

EntireName: Octameric RN1-Fav pore
Components
  • Complex: Octameric RN1-Fav pore
    • Protein or peptide: Actinoporin
  • Ligand: Sphingomyelin C18

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Supramolecule #1: Octameric RN1-Fav pore

SupramoleculeName: Octameric RN1-Fav pore / 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 deletion of 67 residues compared to the wild type. The deletion construct has an additional residue at the N-terminal (S) from the expression system.
Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Orbicella faveolata (invertebrata)
Molecular weightTheoretical: 21.307543 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SELDSENDAA DIAAGTIIAG AELTFGLLQN LLYFFANVNR KCAVGVDNES GFRWQEGSTY FFSGTADENL PYSVSDGYAV LYGPRKTNG PVATGVVGVL AYYIPSIGKT LAVMWSVPFD YNFYQNWWNA KLYSGNQRAD YDHYVDLYYN ANPFKANGWH E RSLGSGLK ...String:
SELDSENDAA DIAAGTIIAG AELTFGLLQN LLYFFANVNR KCAVGVDNES GFRWQEGSTY FFSGTADENL PYSVSDGYAV LYGPRKTNG PVATGVVGVL AYYIPSIGKT LAVMWSVPFD YNFYQNWWNA KLYSGNQRAD YDHYVDLYYN ANPFKANGWH E RSLGSGLK FCGSMSSSGQ 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

Concentration0.8 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: 5147 / Average electron dose: 32.0 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: 2.8000000000000003 µm / Nominal defocus min: 0.4 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: 446027 / 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 88194
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final 3D classificationNumber classes: 4 / 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
Output model

PDB-9eyp:
The structure of octameric pore of RN1 variant of actinoporin Fav

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