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- EMDB-15824: catalytic amyloid fibril formed by Ac-LHLHLRL-amide -

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Basic information

Entry
Database: EMDB / ID: EMD-15824
Titlecatalytic amyloid fibril formed by Ac-LHLHLRL-amide
Map dataelectron density map
Sample
  • Complex: catalytic amyloid
    • Protein or peptide: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
Keywordscatalytic amyloid fibril / protein fibril / zinc binding / prion
Biological speciessynthetic construct (others) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHeerde T / Schmidt M / Faendrich M
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG FA 456/23 Germany
German Research Foundation (DFG)CRC 1279/2 project A03 Germany
CitationJournal: Sci Rep / Year: 2023
Title: Cryo-EM structure of a catalytic amyloid fibril.
Authors: Thomas Heerde / Akanksha Bansal / Matthias Schmidt / Marcus Fändrich /
Abstract: Catalytic amyloid fibrils are novel types of bioinspired, functional materials that combine the chemical and mechanical robustness of amyloids with the ability to catalyze a certain chemical reaction. ...Catalytic amyloid fibrils are novel types of bioinspired, functional materials that combine the chemical and mechanical robustness of amyloids with the ability to catalyze a certain chemical reaction. In this study we used cryo-electron microcopy to analyze the amyloid fibril structure and the catalytic center of amyloid fibrils that hydrolyze ester bonds. Our findings show that catalytic amyloid fibrils are polymorphic and consist of similarly structured, zipper-like building blocks that consist of mated cross-β sheets. These building blocks define the fibril core, which is decorated by a peripheral leaflet of peptide molecules. The observed structural arrangement differs from previously described catalytic amyloid fibrils and yielded a new model of the catalytic center.
History
DepositionSep 16, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15824.png

Downloads & links

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Map

FileDownload / File: emd_15824.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationelectron density map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å		1.04 Å/pix.
x 200 pix.
= 208. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0325
Minimum - Maximum-0.040337805 - 0.07030298
Average (Standard dev.)0.00016307773 (±0.001983874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15824_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: first half-map of the 3D refinement

Fileemd_15824_half_map_1.map
Annotationfirst half-map of the 3D refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: second half-map of the 3D refinement

Fileemd_15824_half_map_2.map
Annotationsecond half-map of the 3D refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : catalytic amyloid

EntireName: catalytic amyloid
Components
  • Complex: catalytic amyloid
    • Protein or peptide: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2

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Supramolecule #1: catalytic amyloid

SupramoleculeName: catalytic amyloid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2

MacromoleculeName: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2 / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 928.179 Da
SequenceString:
(ACE)LHLHLRL(NH2)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration0.0471 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mM(HOCH2)3CNH2Tris(hydroxymethyl)aminomethane
1.0 mMZnCl2Zinccloride

Details: 25 mM Tris(hydroxymethyl)aminomethane (Tris), 1 mM Zincchloride
GridModel: C-flat-1.2/1.3 / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 96 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.75 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.56 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 38413
Segment selectionNumber selected: 38413
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE / Target criteria: correlation coefficient
Output model

PDB-8b3a:
catalytic amyloid fibril formed by Ac-LHLHLRL-amide

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