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- PDB-8uie: Structure of recombinantly assembled murine alpha-synuclein fibrils -

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Basic information

Entry
Database: PDB / ID: 8uie
TitleStructure of recombinantly assembled murine alpha-synuclein fibrils
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / synuclein / Parkinson's disease / neurodegeneration / amyloid / 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 / negative regulation of thrombin-activated receptor signaling pathway / beta-tubulin binding / dopamine metabolic process / cuprous ion binding / response to magnesium ion / response to type II interferon / regulation of neuronal synaptic plasticity / positive regulation of exocytosis / positive regulation of endocytosis / kinesin binding / protein complex oligomerization / phospholipase binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / behavioral response to cocaine / mitochondrial ATP synthesis coupled electron transport / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / positive regulation of synaptic transmission / axon terminus / inclusion body / cellular response to copper ion / Hsp70 protein binding / response to interleukin-1 / negative regulation of protein phosphorylation / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / protein destabilization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / 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 / cell cortex / cellular response to oxidative stress / histone binding / 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: 3.1 Å
AuthorsZhou, Y. / Sokratian, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Michael J. Fox FoundationASAP-020527 United States
CitationJournal: To Be Published
Title: Cryo-EM structure and characterization of recombinantly assembled murine alpha-synuclein fibrils
Authors: Zhou, Y. / Sokratian, A.
History
DepositionOct 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 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
D: Alpha-synuclein
E: Alpha-synuclein
F: Alpha-synuclein
G: Alpha-synuclein
H: Alpha-synuclein
I: Alpha-synuclein
J: Alpha-synuclein
K: Alpha-synuclein
L: Alpha-synuclein
M: Alpha-synuclein


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


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 6 / Rise per n subunits: 4.84 Å / Rotation per n subunits: -0.84 °)

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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(DE3) (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: alpha-synuclein / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4 / Details: Phosphate-buffered saline (PBS)
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMSodium ChlorideNaCl1
22.7 mMPotassium ChlorideKCl1
310 mMSodium Phosphate DibasicNa2HPO41
41.8 mMPotassium Phosphate MonobasicKH2PO41
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293.15 K

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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: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.84 ° / Axial rise/subunit: 4.84 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27523 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL

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