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- EMDB-51420: Structure of 5mer pore intermediate of Sticholysin II (StnII) tox... -

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Basic information

Entry
Database: EMDB / ID: EMD-51420
TitleStructure of 5mer pore intermediate of Sticholysin II (StnII) toxin in lipid nanodiscs
Map data5-mer intermediate pore formation structure of Sticholysin II (StnII) in lipid nanodiscs
Sample
  • Complex: Sticholysin II or DELTA-stichotoxin-She4b (StnII) in lipid nanodiscs
    • Protein or peptide: DELTA-stichotoxin-She4b
  • Ligand: sphingomyelin
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 / extracellular region / identical protein binding
Similarity search - Function
Sea anemone actinoporin-like / : / Sea anemone cytotoxic protein / Cytolysin/lectin
Similarity search - Domain/homology
DELTA-stichotoxin-She4b
Similarity search - Component
Biological speciesStichodactyla helianthus (sea anemone)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMartin Benito J / Santiago C / Carlero D
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117752RB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesTED2021-132748B-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) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51420.png

Downloads & links

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Map

FileDownload / File: emd_51420.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation5-mer intermediate pore formation structure of Sticholysin II (StnII) in lipid nanodiscs
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 180 pix.
= 196.704 Å		1.09 Å/pix.
x 180 pix.
= 196.704 Å		1.09 Å/pix.
x 180 pix.
= 196.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0928 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.185
Minimum - Maximum-0.41908917 - 1.1731051
Average (Standard dev.)0.0053582923 (±0.04070415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 196.70401 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map of the 5-mer intermediate pore formation...

Fileemd_51420_additional_1.map
AnnotationSharpened map of the 5-mer intermediate pore formation structure of Sticholysin II (StnII) in lipid nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of the 5-mer intermediate pore...

Fileemd_51420_half_map_1.map
AnnotationHalf map B of the 5-mer intermediate pore formation structure of Sticholysin II (StnII) in lipid nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of the 5-mer intermediate pore...

Fileemd_51420_half_map_2.map
AnnotationHalf map A of the 5-mer intermediate pore formation structure of Sticholysin II (StnII) in lipid nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sticholysin II or DELTA-stichotoxin-She4b (StnII) in lipid nanodiscs

EntireName: Sticholysin II or DELTA-stichotoxin-She4b (StnII) in lipid nanodiscs
Components
  • Complex: Sticholysin II or DELTA-stichotoxin-She4b (StnII) in lipid nanodiscs
    • Protein or peptide: DELTA-stichotoxin-She4b
  • Ligand: sphingomyelin

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Supramolecule #1: Sticholysin II or DELTA-stichotoxin-She4b (StnII) in lipid nanodiscs

SupramoleculeName: Sticholysin II or DELTA-stichotoxin-She4b (StnII) in lipid nanodiscs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Stichodactyla helianthus (sea anemone)
Molecular weightTheoretical: 192 KDa

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Macromolecule #1: DELTA-stichotoxin-She4b

MacromoleculeName: DELTA-stichotoxin-She4b / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Stichodactyla helianthus (sea anemone)
Molecular weightTheoretical: 19.302844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ALAGTIIAGA SLTFQVLDKV LEELGKVSRK IAVGIDNESG GTWTALNAYF RSGTTDVILP EFVPNTKALL YSGRKDTGPV ATGAVAAFA YYMSSGNTLG VMFSVPFDYN WYSNWWDVKI YSGKRRADQG MYEDLYYGNP YRGDNGWHEK NLGYGLRMKG I MTSAGEAK MQIKISR

UniProtKB: DELTA-stichotoxin-She4b

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Macromolecule #2: sphingomyelin

MacromoleculeName: sphingomyelin / type: ligand / ID: 2 / Number of copies: 8 / Formula: FO4
Molecular weightTheoretical: 814.233 Da
Chemical component information

ChemComp-FO4:
sphingomyelin

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5000000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 272000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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