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- PDB-9eyq: The structure of nonameric pore of RN1 variant of actinoporin Fav -

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Basic information

Entry
Database: PDB / ID: 9eyq
TitleThe structure of nonameric pore of RN1 variant of actinoporin Fav
ComponentsActinoporin
KeywordsTOXIN / Actinoporin / Pore-forming toxin / Pore / nonamer / Transmembrane pore / Protein nanopore
Function / homology:
Function and homology information
Biological speciesOrbicella faveolata (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsSolinc, G. / Srnko, M. / Anderluh, G. / Crnkovic, A. / Podobnik, M.
Funding support Slovenia, 3items
OrganizationGrant numberCountry
Slovenian Research AgencyJ4-8225 Slovenia
Slovenian Research AgencyP1-0391 Slovenia
Other private
CitationJournal: ACS Sens / Year: 2026
Title: High-Throughput Human Histone Detection by an Engineered Actinoporin Nanopore.
Authors: Marija Srnko / Gašper Šolinc / Ana Crnković / Franci Merzel / Michael Jordan / E Jayne Wallace / Marjetka Podobnik / Gregor Anderluh /
Abstract: The use of protein nanopores has proven to be very promising for the identification of proteins or the sequencing of peptides. However, their widespread use in biosensor applications is limited by ...The use of protein nanopores has proven to be very promising for the identification of proteins or the sequencing of peptides. However, their widespread use in biosensor applications is limited by more complex molecular properties of proteins in comparison to nucleic acids. Here, we developed an α-helical Fav nanopore from the coral Orbicella faveolata to detect human histones using a commercial MinION device. The engineered nanopores showed stable insertion into the polymeric membrane support. Bulk analysis of several tens to hundreds of pores per measurement revealed significant differences in mean current passing the pore and current noise resulting from capturing different full-length human histones or their post-translationally modified variants into the pore lumen. Importantly, detailed blocking analyses confirmed histone-specific signals that allow further discrimination between two medically important extracellular histones in mixtures. The newly developed Fav nanopore and high-throughput approach for the detection of biomedically important proteins is an important step towards the widespread use of nanopores in modern analytics.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actinoporin
B: Actinoporin
C: Actinoporin
D: Actinoporin
E: Actinoporin
F: Actinoporin
G: Actinoporin
H: Actinoporin
I: Actinoporin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,71254
Polymers191,7689
Non-polymers32,94445
Water00
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
Actinoporin / RN1-Fav


Mass: 21307.543 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Details: This protein was expressed with an N-terminal deletion of 67 residues compared to the wild type. The deletion construct has three additional residues at the N-terminal (S) from the expression system.
Source: (gene. exp.) Orbicella faveolata (invertebrata) / Plasmid: pET28a (+)
Details (production host): modified pET28a (+) plasmid with the N-terminal 6 histidine tag and TEV restriction site (ENLYFQS)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical...
ChemComp-A1H8M / Sphingomyelin C18 / trimethyl-[2-[[(E,2S,3R)-2-(octadecanoylamino)-3-oxidanyl-octadec-4-enoxy]-oxidanyl-phosphoryl]oxyethyl]azanium


Mass: 732.089 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C41H84N2O6P
Has ligand of interestN
Has protein modificationY

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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: Nonameric RN1-Fav pore / Type: COMPLEX
Details: Nonameric Fav pore prepared on 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC):sphingomyelin (1:1 molar ratio) membranes
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Orbicella faveolata (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Cell: DE3 / Plasmid: pET28a
Buffer solutionpH: 8 / Details: 150 mM NaCl, 50 mM Tris/HCl, 0.02 % Brij 35, pH 8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMTris1
30.02 %Brij 351
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 5147
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
2EPUimage acquisition
4cryoSPARCv4CTF correction
7UCSF ChimeraX1.6model fitting
9Coot0.98model refinement
10PHENIX1.19model refinement
11ISOLDE1.6model refinement
12cryoSPARCV4initial Euler assignment
13cryoSPARCv4final Euler assignment
14cryoSPARCv4classification
15cryoSPARCv43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 446027 / Details: Number of particles after template picking
SymmetryPoint symmetry: C9 (9 fold cyclic)
3D reconstructionResolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97704 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingDetails: Pore structure of the same protein from related entries
Source name: Other / Type: experimental model

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