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- PDB-9gkl: Structure of the octameric pore of Fragaceotxin C (FraC or DELTA-... -

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Basic information

Entry
Database: PDB / ID: 9gkl
TitleStructure of the octameric pore of Fragaceotxin C (FraC or DELTA-actitoxin-Afr1a) in large unilamellar vesicles.
ComponentsDELTA-actitoxin-Afr1a
KeywordsMEMBRANE PROTEIN / LUVs / 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
CHOLESTEROL / sphingomyelin / DELTA-actitoxin-Afr1a
Similarity search - Component
Biological speciesActinia fragacea (sea anemone)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsMartin Benito, J. / Santiago, C. / Carlero, D. / Arranz, R.
Funding support Spain, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: DELTA-actitoxin-Afr1a
A: DELTA-actitoxin-Afr1a
B: DELTA-actitoxin-Afr1a
C: DELTA-actitoxin-Afr1a
D: DELTA-actitoxin-Afr1a
E: DELTA-actitoxin-Afr1a
F: DELTA-actitoxin-Afr1a
G: DELTA-actitoxin-Afr1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,272112
Polymers157,2748
Non-polymers70,998104
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
DELTA-actitoxin-Afr1a / DELTA-AITX-Afr1a / Alpha-helical pore-forming toxin / PFT / Cytolysin / Fragaceatoxin C / fraC


Mass: 19659.225 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinia fragacea (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: B9W5G6
#2: Chemical...
ChemComp-FO4 / sphingomyelin


Mass: 814.233 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C47H94N2O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of the octameric pore of Fragaceotxin C (FraC or DELTA-actitoxin-Afr1a) in large unilamellar vesicles
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.192 MDa / Experimental value: NO
Source (natural)Organism: Stichodactyla helianthus (sea anemone)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Xmippparticle selection
2PHENIX1.21_5207model refinement
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 22000000
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122000
Details: Resolution calculated with cryoSPARC using the tight mask.
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.53 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005814728
ELECTRON MICROSCOPYf_angle_d0.733819744
ELECTRON MICROSCOPYf_chiral_restr0.05341992
ELECTRON MICROSCOPYf_plane_restr0.00422096
ELECTRON MICROSCOPYf_dihedral_angle_d16.73425832

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