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- PDB-9ewv: mouse alpha-synuclein -

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Basic information

Entry
Database: PDB / ID: 9ewv
Titlemouse alpha-synuclein
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / recombinant / fibril
Function / homology
Function and homology information


PKR-mediated signaling / regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / platelet alpha granule membrane / membrane organization / neurotransmitter secretion / synaptic transmission, dopaminergic / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission ...PKR-mediated signaling / regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / platelet alpha granule membrane / membrane organization / neurotransmitter secretion / synaptic transmission, dopaminergic / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / nuclear outer membrane / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of reactive oxygen species metabolic process / arachidonate binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein complex oligomerization / negative regulation of thrombin-activated receptor signaling pathway / beta-tubulin binding / dopamine metabolic process / cuprous ion binding / response to type II interferon / regulation of neuronal synaptic plasticity / positive regulation of exocytosis / kinesin binding / positive regulation of endocytosis / phospholipase binding / behavioral response to cocaine / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrial ATP synthesis coupled electron transport / response to magnesium ion / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / positive regulation of synaptic transmission / phospholipid metabolic process / axon terminus / inclusion body / cellular response to copper ion / Hsp70 protein binding / response to interleukin-1 / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / negative regulation of protein phosphorylation / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / cytoplasmic vesicle membrane / tau protein binding / terminal bouton / receptor internalization / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / presynapse / actin binding / cellular response to oxidative stress / histone binding / cell cortex / growth cone / microtubule binding / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / postsynapse / response to lipopolysaccharide / mitochondrial inner membrane
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTatli, M. / Stahlberg, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_188548 Switzerland
CitationJournal: Sci Adv / Year: 2024
Title: Mouse α-synuclein fibrils are structurally and functionally distinct from human fibrils associated with Lewy body diseases.
Authors: Arpine Sokratian / Ye Zhou / Meltem Tatli / Kevin J Burbidge / Enquan Xu / Elizabeth Viverette / Sonia Donzelli / Addison M Duda / Yuan Yuan / Huizhong Li / Samuel Strader / Nirali Patel / ...Authors: Arpine Sokratian / Ye Zhou / Meltem Tatli / Kevin J Burbidge / Enquan Xu / Elizabeth Viverette / Sonia Donzelli / Addison M Duda / Yuan Yuan / Huizhong Li / Samuel Strader / Nirali Patel / Lauren Shiell / Tuyana Malankhanova / Olivia Chen / Joseph R Mazzulli / Lalith Perera / Henning Stahlberg / Mario Borgnia / Alberto Bartesaghi / Hilal A Lashuel / Andrew B West /
Abstract: The intricate process of α-synuclein aggregation and fibrillization holds pivotal roles in Parkinson's disease (PD) and multiple system atrophy (MSA). While mouse α-synuclein can fibrillize in ...The intricate process of α-synuclein aggregation and fibrillization holds pivotal roles in Parkinson's disease (PD) and multiple system atrophy (MSA). While mouse α-synuclein can fibrillize in vitro, whether these fibrils commonly used in research to induce this process or form can reproduce structures in the human brain remains unknown. Here, we report the first atomic structure of mouse α-synuclein fibrils, which was solved in parallel by two independent teams. The structure shows striking similarity to MSA-amplified and PD-associated E46K fibrils. However, mouse α-synuclein fibrils display altered packing arrangements, reduced hydrophobicity, and heightened fragmentation sensitivity and evoke only weak immunological responses. Furthermore, mouse α-synuclein fibrils exhibit exacerbated pathological spread in neurons and humanized α-synuclein mice. These findings provide critical insights into the structural underpinnings of α-synuclein pathogenicity and emphasize a need to reassess the role of mouse α-synuclein fibrils in the development of related diagnostic probes and therapeutic interventions.
History
DepositionApr 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-synuclein
B: Alpha-synuclein
C: Alpha-synuclein
D: Alpha-synuclein
E: Alpha-synuclein
I: Alpha-synuclein
F: Alpha-synuclein
G: Alpha-synuclein
H: Alpha-synuclein
J: Alpha-synuclein
K: Alpha-synuclein
L: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)174,01412
Polymers174,01412
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 14501.185 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snca, Syn
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O55042
Has protein modificationN

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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: Mouse alpha-synuclein fibrils / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 10 kDa/nm / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Plasmid: pT7-7
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMsodium chlorideNaCl1
22.7 mMpotasium chlorideKCl1
310 mMDisodium phosphateNa2HPO1
41.8 mMMonopotassium phosphateKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: in PBS, sonicated sample
Specimen supportGrid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5358

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_5109 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.6 ° / Axial rise/subunit: 2.39 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 146075
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50378 / Symmetry type: HELICAL
Atomic model buildingB value: 51.895 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: 0.759261
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0095388
ELECTRON MICROSCOPYf_angle_d0.9237272
ELECTRON MICROSCOPYf_dihedral_angle_d15.091860
ELECTRON MICROSCOPYf_chiral_restr0.058948
ELECTRON MICROSCOPYf_plane_restr0.003900

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