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- EMDB-53305: Cryo-EM Structure of catalytic amyloids -

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Basic information

Entry
Database: EMDB / ID: EMD-53305
TitleCryo-EM Structure of catalytic amyloids
Map data3D reconstruction of PFK with nitrocefin
Sample
  • Complex: Amyloid coiled-coil fibrils
    • Protein or peptide: Amyloid coiled-coil fibrils
KeywordsAllosteric amyloid coiled-coil fibrils / PROTEIN FIBRIL
Biological speciesAnaeramoeba ignava (eukaryote)
Methodhelical reconstruction / cryo EM / Resolution: 5.0 Å
AuthorsZalk R / Kunnath SM / Arad E / Jelinek R
Funding support Israel, 1 items
OrganizationGrant numberCountry
Other private Israel
CitationJournal: Nat Commun / Year: 2025
Title: Allosteric amyloid catalysis by coiled coil fibrils.
Authors: Sisira Mambram Kunnath / Elad Arad / Ran Zalk / Itamar Kass / Anat Shahar / Albert Batushansky / Hanna Rapaport / Raz Jelinek /
Abstract: Amyloid-mediated catalysis of key biological reactions has recently attracted significant interest as this phenomenon may portend new functions for physiological and synthetic amyloid proteins. Here, ...Amyloid-mediated catalysis of key biological reactions has recently attracted significant interest as this phenomenon may portend new functions for physiological and synthetic amyloid proteins. Here, we report an allosteric mechanism of catalytic amyloids, mediated via an unconventional coiled-coil fibril organization, facilitating hydrolysis of β-lactam antibiotics. Specifically, the hydrolysis reaction was catalyzed by a fibrillar peptide comprising alternating lysine/phenylalanine β-sheet-forming sequence. Analysis of peptide variants, simulations, and cryogenic electron microscopy reveal that the β-lactam molecules attach electrostatically to the lysine sidechains on the fibrils' surfaces, generating a double-coiled fibril structure in which the anchored β-lactam molecules are nestled within twisted fibril strands. This organization facilitates the allosteric catalytic process in which hydrolytic β-lactam ring opening is induced via nucleophilic attacks by the lysine sidechains degradation. The allosteric catalytic activity of the phenylalanine/lysine amyloid fibrils highlights the functional versatility of amyloid fibrils and their potential applications in human health and environmental biotechnology.
History
DepositionApr 1, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53305.png

Downloads & links

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Map

FileDownload / File: emd_53305.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of PFK with nitrocefin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 500 pix.
= 445. Å		0.89 Å/pix.
x 500 pix.
= 445. Å		0.89 Å/pix.
x 500 pix.
= 445. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.09488874 - 0.1328811
Average (Standard dev.)0.00035813352 (±0.010071334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 445.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: 3D reconstruction of PFK with nitrocefin HalfB

Fileemd_53305_half_map_1.map
Annotation3D reconstruction of PFK with nitrocefin HalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D reconstruction of PFK with nitrocefin HalfA

Fileemd_53305_half_map_2.map
Annotation3D reconstruction of PFK with nitrocefin HalfA
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 coiled-coil fibrils

EntireName: Amyloid coiled-coil fibrils
Components
  • Complex: Amyloid coiled-coil fibrils
    • Protein or peptide: Amyloid coiled-coil fibrils

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Supramolecule #1: Amyloid coiled-coil fibrils

SupramoleculeName: Amyloid coiled-coil fibrils / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Anaeramoeba ignava (eukaryote)

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Macromolecule #1: Amyloid coiled-coil fibrils

MacromoleculeName: Amyloid coiled-coil fibrils / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Anaeramoeba ignava (eukaryote)
SequenceString:
PKFKFKFKFK FKP

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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

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsSpherical aberration corrector: 2.7 mm / Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 12.0 Å
Applied symmetry - Helical parameters - Δ&Phi: -7.353 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 507432
CTF correctionType: NONE
Startup modelType of model: OTHER / Details: cylinder
Final angle assignmentType: NOT APPLICABLE

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