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

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Basic information

Entry
Database: PDB / ID: 8b3a
Titlecatalytic amyloid fibril formed by Ac-LHLHLRL-amide
ComponentsACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
KeywordsPROTEIN FIBRIL / catalytic amyloid fibril / zinc binding / prion
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHeerde, T. / Schmidt, M. / Faendrich, M.
Funding support Germany, 2items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
B: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
C: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
D: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
E: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
F: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
G: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
H: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
I: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
J: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
K: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
L: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
M: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
N: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
O: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
P: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
Q: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
R: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
S: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
T: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
U: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
V: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
W: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
X: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
Y: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
Z: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
a: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
b: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
c: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2
d: ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2


Theoretical massNumber of molelcules
Total (without water)27,84530
Polymers27,84530
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide ...
ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2


Mass: 928.179 Da / Num. of mol.: 30 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: catalytic amyloid / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Details: 25 mM Tris(hydroxymethyl)aminomethane (Tris), 1 mM Zincchloride
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris(hydroxymethyl)aminomethane(HOCH2)3CNH21
21 mMZincclorideZnCl21
SpecimenConc.: 0.0471 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 96 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 12 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
7Coot0.8.9model fitting
9PHENIX1.16-3549model refinement
12RELION3.0.4classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.56 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C2
Particle selectionNum. of particles selected: 38413
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38413 / Symmetry type: HELICAL
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient

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