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- EMDB-52185: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Poly... -

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Basic information

Entry
Database: EMDB / ID: EMD-52185
TitleAmyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.3L
Map data
Sample
  • Complex: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.3L
    • Protein or peptide: Citropin-1.3
KeywordsAmyloid Helical / ANTIMICROBIAL PROTEIN
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsStrati F / Pigozzi CM / Bloch Y / Rayan B / Mostafavi S / Monistrol J / Golubev A / Gustavsson E / Landau M
Funding supportEuropean Union, United States, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101087140European Union
Other private United States
CitationJournal: To Be Published
Title: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.3L
Authors: Strati F / Pigozzi CM / Bloch Y / Rayan B / Mostafavi S / Monistrol J / Golubev A / Gustavsson E / Landau M
History
DepositionNov 25, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52185.png

Downloads & links

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Map

FileDownload / File: emd_52185.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 250.5 Å		0.84 Å/pix.
x 300 pix.
= 250.5 Å		0.84 Å/pix.
x 300 pix.
= 250.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.0037151682 - 0.009383525
Average (Standard dev.)-0.00007304525 (±0.0005689711)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 250.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52185_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52185_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52185_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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.3L
Components
  • Complex: Amyloid fibril from the antimicrobial peptide citropin 1-3 - Polymorph Nr.3L
    • Protein or peptide: Citropin-1.3

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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.3L
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ranoidea citropa (Blue Mountains treefrog)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Citropin-1.3

MacromoleculeName: Citropin-1.3 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Ranoidea citropa (Blue Mountains treefrog)
Molecular weightTheoretical: 1.631998 KDa
SequenceString:
GLFDIIKKVA SVIGGL

UniProtKB: Citropin-1.3

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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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 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: 4.74 Å
Applied symmetry - Helical parameters - Δ&Phi: -5.47 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49778
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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