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- EMDB-52261: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly... -

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Basic information

Entry
Database: EMDB / ID: EMD-52261
TitleAmyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.1
Map data
Sample
  • Complex: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.1
KeywordsAmyloid Helical / ANTIMICROBIAL PROTEIN
Biological speciesRanoidea citropa (Blue Mountains treefrog)
Methodhelical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsStrati F / Cali PM / Bloch Y / Rayan B / Monistrol J / Golubev A / Siavash M / Gustavsson E / Landau M
Funding supportEuropean Union, United States, 2 items
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
DepositionDec 5, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52261.png

Downloads & links

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Map

FileDownload / File: emd_52261.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 686 pix.
= 583.1 Å		0.85 Å/pix.
x 686 pix.
= 583.1 Å		0.85 Å/pix.
x 686 pix.
= 583.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.029724548 - 0.0812162
Average (Standard dev.)-0.000028506554 (±0.0040248446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions686686686
Spacing686686686
CellA=B=C: 583.10004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_52261_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52261_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly...

EntireName: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.1
Components
  • Complex: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.1

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Supramolecule #1: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly...

SupramoleculeName: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ranoidea citropa (Blue Mountains treefrog)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 0.01 Å
Applied symmetry - Helical parameters - Δ&Phi: 0 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1412454
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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