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- PDB-9r7e: Cryo-EM Structure of catalytic amyloids -

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Basic information

Entry
Database: PDB / ID: 9r7e
TitleCryo-EM Structure of catalytic amyloids
ComponentsPRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
KeywordsPROTEIN FIBRIL / Allosteric amyloid coiled-coil fibrils
Function / homologyNitrocefin - open form
Function and homology information
Biological speciesAnaeramoeba ignava (eukaryote)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5 Å
AuthorsShahar, A. / Zalk, R. / Arad, E.
Funding support Israel, 1items
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
DepositionMay 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
B: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
C: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
D: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
E: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
F: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
G: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
L: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
M: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
N: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
O: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
P: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
Q: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
R: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
S: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
T: PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,70920
Polymers27,57116
Non-polymers2,1384
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
PRO-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PHE-LYS-PRO


Mass: 1723.192 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Anaeramoeba ignava (eukaryote)
#2: Chemical
ChemComp-NEF / Nitrocefin - open form / (2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 534.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H18N4O9S2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: PFK / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Anaeramoeba ignava (eukaryote)
Source (recombinant)Organism: Anaeramoeba ignava (eukaryote)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: 4.6.0 / Category: 3D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -7.353 ° / Axial rise/subunit: 12 Å / Axial symmetry: C1
3D reconstructionResolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 507432 / Symmetry type: HELICAL

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