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- PDB-8ol5: Murine type II Abeta fibril from ARTE10 mouse -

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Basic information

Entry
Database: PDB / ID: 8ol5
TitleMurine type II Abeta fibril from ARTE10 mouse
ComponentsAmyloid-beta protein 42
KeywordsPROTEIN FIBRIL / Amyloid fibril
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / regulation of synapse structure or activity / positive regulation of synaptic transmission, cholinergic / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / PTB domain binding / Golgi-associated vesicle / astrocyte projection / neuron remodeling / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / dendrite development / regulation of multicellular organism growth / nuclear envelope lumen / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / intracellular copper ion homeostasis / Notch signaling pathway / main axon / ECM proteoglycans / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / adult locomotory behavior / extracellular matrix organization / neuronal dense core vesicle / regulation of long-term neuronal synaptic plasticity / swimming behavior / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of calcium-mediated signaling / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / neuron projection maintenance / clathrin-coated pit / visual learning / astrocyte activation / cellular response to cAMP / synaptic cleft / regulation of neuron apoptotic process / Mitochondrial protein degradation / ionotropic glutamate receptor signaling pathway / positive regulation of glycolytic process / learning / platelet alpha granule lumen / response to interleukin-1 / locomotory behavior / cellular response to copper ion / endosome lumen / trans-Golgi network membrane / positive regulation of interleukin-1 beta production / dendritic shaft / central nervous system development / positive regulation of long-term synaptic potentiation / protein serine/threonine kinase binding / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / microglial cell activation / cellular response to nerve growth factor stimulus / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / synapse organization / positive regulation of interleukin-6 production / positive regulation of JNK cascade / recycling endosome / response to lead ion / endocytosis / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cellular response to amyloid-beta / calcium ion transport / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / regulation of gene expression / regulation of translation
Similarity search - Function
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZielinski, M. / Peralta Reyes, F.S. / Gremer, L. / Schemmert, S. / Frieg, B. / Willuweit, A. / Donner, L. / Elvers, M. / Nilsson, L.N.G. / Syvanen, S. ...Zielinski, M. / Peralta Reyes, F.S. / Gremer, L. / Schemmert, S. / Frieg, B. / Willuweit, A. / Donner, L. / Elvers, M. / Nilsson, L.N.G. / Syvanen, S. / Sehlin, D. / Ingelsson, M. / Willbold, D. / Schroeder, G.F.
Funding support Germany, Sweden, 5items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research16LW028 Germany
Swedish Research Council2021-02793 Sweden
Swedish Research Council2021-01083 Sweden
Swedish Research Council2021-03524 Sweden
Helmholtz Association Germany
CitationJournal: Nat Neurosci / Year: 2023
Title: Cryo-EM of Aβ fibrils from mouse models find tg-APP fibrils resemble those found in patients with sporadic Alzheimer's disease.
Authors: Mara Zielinski / Fernanda S Peralta Reyes / Lothar Gremer / Sarah Schemmert / Benedikt Frieg / Luisa U Schäfer / Antje Willuweit / Lili Donner / Margitta Elvers / Lars N G Nilsson / Stina ...Authors: Mara Zielinski / Fernanda S Peralta Reyes / Lothar Gremer / Sarah Schemmert / Benedikt Frieg / Luisa U Schäfer / Antje Willuweit / Lili Donner / Margitta Elvers / Lars N G Nilsson / Stina Syvänen / Dag Sehlin / Martin Ingelsson / Dieter Willbold / Gunnar F Schröder /
Abstract: The use of transgenic mice displaying amyloid-β (Aβ) brain pathology has been essential for the preclinical assessment of new treatment strategies for Alzheimer's disease. However, the properties ...The use of transgenic mice displaying amyloid-β (Aβ) brain pathology has been essential for the preclinical assessment of new treatment strategies for Alzheimer's disease. However, the properties of Aβ in such mice have not been systematically compared to Aβ in the brains of patients with Alzheimer's disease. Here, we determined the structures of nine ex vivo Aβ fibrils from six different mouse models by cryogenic-electron microscopy. We found novel Aβ fibril structures in the APP/PS1, ARTE10 and tg-SwDI models, whereas the human type II filament fold was found in the ARTE10, tg-APP and APP23 models. The tg-APP mice showed an Aβ fibril whose structure resembles the human type I filament found in patients with sporadic Alzheimer's disease. A detailed assessment of the Aβ fibril structure is key to the selection of adequate mouse models for the preclinical development of novel plaque-targeting therapeutics and positron emission tomography imaging tracers in Alzheimer's disease.
History
DepositionMar 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Amyloid-beta protein 42
E: Amyloid-beta protein 42
A: Amyloid-beta protein 42
B: Amyloid-beta protein 42
C: Amyloid-beta protein 42
D: Amyloid-beta protein 42
F: Amyloid-beta protein 42
G: Amyloid-beta protein 42
I: Amyloid-beta protein 42
J: Amyloid-beta protein 42


Theoretical massNumber of molelcules
Total (without water)45,20110
Polymers45,20110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21000 Å2
ΔGint-85 kcal/mol
Surface area11750 Å2

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Components

#1: Protein/peptide
Amyloid-beta protein 42 / Abeta42 / Beta-APP42


Mass: 4520.087 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APP, A4, AD1 / Organ: Brain / Production host: Mus musculus (house mouse) / Strain (production host): ARTE10 / References: UniProt: P05067

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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: Amyloid fibril of amyloid-beta / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 20 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9521

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
4CTFFINDCTF correction
9PHENIX1.20.1model refinement
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -3.21 ° / Axial rise/subunit: 4.76 Å / Axial symmetry: C2
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226920 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL

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