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- PDB-9hi8: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly... -

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Basic information

Entry
Database: PDB / ID: 9hi8
TitleAmyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.3L
ComponentsCitropin-1.3
KeywordsANTIMICROBIAL PROTEIN / Amyloid Helical
Function / homologyAurein antibiotic peptide family / Aurein-like antibiotic peptide / defense response to bacterium / extracellular region / Citropin-1.3
Function and homology information
Biological speciesRanoidea citropa (Blue Mountains treefrog)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsStrati, F. / Pigozzi, C.M. / Bloch, Y. / Rayan, B. / Mostafavi, S. / Monistrol, J. / Golubev, A. / Gustavsson, E. / Landau, M.
Funding supportEuropean Union, United States, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101087140European Union
Other private United States
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Structural and Functional Versatility of the Amyloidogenic Non-Amidated Variant of the Antimicrobial Peptide Citropin 1.3.
Authors: Fabio Strati / Mariana Pigozzi Cali / Yehudi Bloch / Siavash Mostafavi / Jim Monistrol / Aleksandr Golubev / Bader Rayan / Emil Gustavsson / Meytal Landau /
Abstract: Citropin 1.3 is an antimicrobial peptide secreted by the amphibian Litoria citropa (Southern bell frog). In this study, the structural and functional properties of its non-amidated form, which self- ...Citropin 1.3 is an antimicrobial peptide secreted by the amphibian Litoria citropa (Southern bell frog). In this study, the structural and functional properties of its non-amidated form, which self-assembles into distinct fibrillar architectures, are investigated. Using cryogenic electron microscopy, X-ray crystallography, and fluorescence microscopy with model membranes and cells, diverse supramolecular structures, including canonical amyloid fibrils, multilayered nanotubes, and a novel mixed fibril type, are identified. In giant unilamellar vesicles, citropin 1.3 promoted membrane fusion and underwent lipid-induced phase separation. In mammalian cells, it permeabilized membranes, induced cell death, and colocalized with nucleic acids. These findings link antimicrobial activity to amyloid assembly and highlight the peptide's structural plasticity and potential biological functions, offering new insights into amyloid-based antimicrobial mechanisms.
History
DepositionNov 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 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: Citropin-1.3
B: Citropin-1.3
C: Citropin-1.3
D: Citropin-1.3
E: Citropin-1.3
F: Citropin-1.3


Theoretical massNumber of molelcules
Total (without water)9,7926
Polymers9,7926
Non-polymers00
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/peptide
Citropin-1.3


Mass: 1631.998 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Ranoidea citropa (Blue Mountains treefrog) / References: UniProt: P81846
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.3L
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.16 MDa / Experimental value: YES
Source (natural)Organism: Ranoidea citropa (Blue Mountains treefrog)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -5.47 ° / Axial rise/subunit: 4.74 Å / Axial symmetry: C2
3D reconstructionResolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49778 / Symmetry type: HELICAL

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