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- EMDB-51432: Structure of fragacetoxin C in lipid nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-51432
TitleStructure of fragacetoxin C in lipid nanodiscs
Map dataStructure of the octameric pore of Fragaceotxin C (FraC or DELTA-actitoxin-Afr1a) on lipid nanodiscs.
Sample
  • Complex: Octameric pore in nanodiscs
    • Protein or peptide: DELTA-actitoxin-Afr1a
  • Ligand: sphingomyelin
  • Ligand: CHOLESTEROL
  • Ligand: water
Keywordsmembrane protein / nanodisc / toxin / actinoporin
Function / homology
Function and homology information


nematocyst / pore complex assembly / cytolysis in another organism / other organism cell membrane / pore complex / monoatomic cation transport / channel activity / toxin activity / lipid binding / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / : / Sea anemone cytotoxic protein / Cytolysin/lectin
Similarity search - Domain/homology
DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsMartin Benito J / Santiago C
Funding support Spain, 3 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117752RB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesTED2021-132748B-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2024-162190OB-I00 Spain
CitationJournal: Sci Adv / Year: 2025
Title: Elucidating the structure and assembly mechanism of actinoporin pores in complex membrane environments.
Authors: Rocío Arranz / César Santiago / Simonas Masiulis / Esperanza Rivera-de-Torre / Juan Palacios-Ortega / Diego Carlero / Diego Heras-Márquez / José G Gavilanes / Ernesto Arias-Palomo / ...Authors: Rocío Arranz / César Santiago / Simonas Masiulis / Esperanza Rivera-de-Torre / Juan Palacios-Ortega / Diego Carlero / Diego Heras-Márquez / José G Gavilanes / Ernesto Arias-Palomo / Álvaro Martínez-Del-Pozo / Sara García-Linares / Jaime Martín-Benito /
Abstract: Pore-forming proteins exemplify the transformative potential of biological molecules. Produced as soluble monomers, they assemble into multimeric membrane-inserted complexes in response to specific ...Pore-forming proteins exemplify the transformative potential of biological molecules. Produced as soluble monomers, they assemble into multimeric membrane-inserted complexes in response to specific membrane environments. Actinoporins, a class of pore-forming proteins from sea anemones, target membranes to kill cells. Here, we report cryogenic electron microscopy structures of two actinoporins, fragaceatoxin C and sticholysin II, reconstituted in lipid membranes. The structures reveal an ordered arrangement of dozens of lipid molecules that form an integral part of the pore architecture. We also captured distinct oligomeric intermediates, arc-shaped assemblies with monomers in transitional conformations, representing key snapshots along the pore formation pathway. These data provide direct structural evidence for a stepwise mechanism in which monomers sequentially bind the membrane and undergo conformational changes that drive pore assembly and membrane disruption. Our findings reveal how these proteins reshape membranes and offer mechanistic insights into their cytolytic activity. This work broadens our understanding of pore-forming proteins, which are gaining increasing relevance in diverse biotechnological applications.
History
DepositionAug 25, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51432.png

Downloads & links

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Map

FileDownload / File: emd_51432.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the octameric pore of Fragaceotxin C (FraC or DELTA-actitoxin-Afr1a) on lipid nanodiscs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 140 pix.
= 148.4 Å		1.06 Å/pix.
x 140 pix.
= 148.4 Å		1.06 Å/pix.
x 140 pix.
= 148.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.5407961 - 1.6923462
Average (Standard dev.)0.017053291 (±0.12922071)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 148.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Structure of the octameric pore of Fragaceotxin C...

Fileemd_51432_additional_1.map
AnnotationStructure of the octameric pore of Fragaceotxin C (FraC or DELTA-actitoxin-Afr1a) on lipid nanodiscs. Sharp map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of the octameric pore of Fragaceotxin C...

Fileemd_51432_half_map_1.map
AnnotationStructure of the octameric pore of Fragaceotxin C (FraC or DELTA-actitoxin-Afr1a) on lipid nanodiscs. Half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Structure of the octameric pore of Fragaceotxin C...

Fileemd_51432_half_map_2.map
AnnotationStructure of the octameric pore of Fragaceotxin C (FraC or DELTA-actitoxin-Afr1a) on lipid nanodiscs. Half 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 pore in nanodiscs

EntireName: Octameric pore in nanodiscs
Components
  • Complex: Octameric pore in nanodiscs
    • Protein or peptide: DELTA-actitoxin-Afr1a
  • Ligand: sphingomyelin
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: Octameric pore in nanodiscs

SupramoleculeName: Octameric pore in nanodiscs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Actinia fragacea (sea anemone)
Molecular weightTheoretical: 192 KDa

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Macromolecule #1: DELTA-actitoxin-Afr1a

MacromoleculeName: DELTA-actitoxin-Afr1a / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Actinia fragacea (sea anemone)
Molecular weightTheoretical: 19.659225 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ADVAGAVIDG AGLGFDVLKT VLEALGNVKR KIAVGIDNES GKTWTAMNTY FRSGTSDIVL PHKVAHGKAL LYNGQKNRGP VATGVVGVI AYSMSDGNTL AVLFSVPYDY NWYSNWWNVR VYKGQKRADQ RMYEELYYHR SPFRGDNGWH SRGLGYGLKS R GFMNSSGH AILEIHVTKA

UniProtKB: DELTA-actitoxin-Afr1a

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Macromolecule #2: sphingomyelin

MacromoleculeName: sphingomyelin / type: ligand / ID: 2 / Number of copies: 64 / Formula: FO4
Molecular weightTheoretical: 814.233 Da
Chemical component information

ChemComp-FO4:
sphingomyelin

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 32 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
GridModel: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 24000 / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 25000000
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio model usig Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC

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