+Open data
-Basic information
Entry | Database: PDB / ID: 8ot3 | ||||||
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Title | unseeded Abeta(1-40) amyloid fibril (morphology ii) | ||||||
Components | Amyloid-beta A4 protein | ||||||
Keywords | PROTEIN FIBRIL / Amyloid fibril / Amyloid-beta | ||||||
Function / homology | Function and homology information signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft ...signaling receptor activator activity / Golgi-associated vesicle / clathrin-coated pit / axonogenesis / central nervous system development / heparin binding / growth cone / perikaryon / early endosome / membrane raft / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.73 Å | ||||||
Authors | Pfeiffer, P.B. / Schmidt, M. / Faendrich, M. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J Mol Biol / Year: 2024 Title: Cryo-EM Analysis of the Effect of Seeding with Brain-derived Aβ Amyloid Fibrils. Authors: Peter Benedikt Pfeiffer / Marijana Ugrina / Nadine Schwierz / Christina J Sigurdson / Matthias Schmidt / Marcus Fändrich / Abstract: Aβ amyloid fibrils from Alzheimer's brain tissue are polymorphic and structurally different from typical in vitro formed Aβ fibrils. Here, we show that brain-derived (ex vivo) fibril structures can ...Aβ amyloid fibrils from Alzheimer's brain tissue are polymorphic and structurally different from typical in vitro formed Aβ fibrils. Here, we show that brain-derived (ex vivo) fibril structures can be proliferated by seeding in vitro. The proliferation reaction is only efficient for one of the three abundant ex vivo Aβ fibril morphologies, which consists of two peptide stacks, while the inefficiently proliferated fibril morphologies contain four or six peptide stacks. In addition to the seeded fibril structures, we find that de novo nucleated fibril structures can emerge in seeded samples if the seeding reaction is continued over multiple generations. These data imply a competition between de novo nucleation and seed extension and suggest further that seeding favours the outgrowth of fibril morphologies that contain fewer peptide stacks. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ot3.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ot3.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ot3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ot3_validation.pdf.gz | 1017 KB | Display | wwPDB validaton report |
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Full document | 8ot3_full_validation.pdf.gz | 1016.5 KB | Display | |
Data in XML | 8ot3_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 8ot3_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/8ot3 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/8ot3 | HTTPS FTP |
-Related structure data
Related structure data | 17167MC 8ot1C 8ot4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein/peptide | Mass: 4335.852 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: B4DM00 |
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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: in vitro Abeta(1-40) amyloid fibril / Type: COMPLEX / Details: morphology ii / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: RV308 |
Buffer solution | pH: 7.4 |
Buffer component | Conc.: 100 mM / Name: Disodium phosphate / Formula: Na2HPO4 |
Specimen | Conc.: 0.005 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 |
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 95 % |
-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 magnification: 130000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 2.9 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4628 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 179.526 ° / Axial rise/subunit: 2.372 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 41423 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40968 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: BACKBONE TRACE / Space: REAL / Target criteria: correlation coefficient |