+Open data
-Basic information
Entry | Database: PDB / ID: 8b3a | |||||||||
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Title | catalytic amyloid fibril formed by Ac-LHLHLRL-amide | |||||||||
Components | ACE-LEU-HIS-LEU-HIS-LEU-ARG-LEU-NH2 | |||||||||
Keywords | PROTEIN FIBRIL / catalytic amyloid fibril / zinc binding / prion | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Heerde, T. / Schmidt, M. / Faendrich, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b3a.cif.gz | 47.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b3a.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 8b3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b3a_validation.pdf.gz | 922.1 KB | Display | wwPDB validaton report |
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Full document | 8b3a_full_validation.pdf.gz | 921.8 KB | Display | |
Data in XML | 8b3a_validation.xml.gz | 19 KB | Display | |
Data in CIF | 8b3a_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/8b3a ftp://data.pdbj.org/pub/pdb/validation_reports/b3/8b3a | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein/peptide | Mass: 928.179 Da / Num. of mol.: 30 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: catalytic amyloid / Type: COMPLEX / Entity ID: all / Source: NATURAL | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: synthetic construct (others) | |||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | |||||||||||||||
Buffer solution | pH: 8 Details: 25 mM Tris(hydroxymethyl)aminomethane (Tris), 1 mM Zincchloride | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.0471 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 96 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 12 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -0.56 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C2 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 38413 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38413 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient |