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- PDB-9rb3: A53T alpha-synuclein fibril - Type 1 -

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Basic information

Entry
Database: PDB / ID: 9rb3
TitleA53T alpha-synuclein fibril - Type 1
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / fibril / A53T mutant
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of synaptic vesicle recycling ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / negative regulation of platelet-derived growth factor receptor signaling pathway / regulation of glutamate secretion / Lewy body / dopamine biosynthetic process / response to iron(II) ion / negative regulation of thrombin-activated receptor signaling pathway / SNARE complex assembly / positive regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of locomotion / negative regulation of microtubule polymerization / regulation of norepinephrine uptake / synaptic vesicle priming / transporter regulator activity / synaptic vesicle transport / protein kinase inhibitor activity / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / mitochondrial ATP synthesis coupled electron transport / positive regulation of receptor recycling / dynein complex binding / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / negative regulation of serotonin uptake / response to type II interferon / synaptic vesicle endocytosis / kinesin binding / regulation of presynapse assembly / cysteine-type endopeptidase inhibitor activity / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / cellular response to fibroblast growth factor stimulus / phospholipid metabolic process / inclusion body / cellular response to epinephrine stimulus / Hsp70 protein binding / enzyme inhibitor activity / axon terminus / response to interleukin-1 / regulation of microtubule cytoskeleton organization / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / adult locomotory behavior / glutathione metabolic process / excitatory postsynaptic potential / protein tetramerization / protein sequestering activity / tubulin binding / phosphoprotein binding / microglial cell activation / ferrous iron binding / fatty acid metabolic process / synapse organization / PKR-mediated signaling / regulation of long-term neuronal synaptic plasticity / receptor internalization / phospholipid binding / protein destabilization / tau protein binding / enzyme activator activity / terminal bouton / positive regulation of inflammatory response / long-term synaptic potentiation / synaptic vesicle membrane / actin cytoskeleton / growth cone / actin binding / neuron apoptotic process / cellular response to oxidative stress / cell cortex / histone binding / response to lipopolysaccharide / microtubule binding / amyloid fibril formation / chemical synaptic transmission
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSo, R.W.L. / Frieg, B. / Schroeder, G.F. / Watts, J.C.
Funding support Canada, Germany, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Helmholtz Association Germany
CitationJournal: Neuron / Year: 2026
Title: Stochastic misfolding drives the emergence of distinct α-synuclein strains.
Authors: Raphaella W L So / Benedikt Frieg / José D Camino / Christopher Situ / Mark N Metri / Nicholas R G Silver / Le Yao Li / Alison Mao / Erica Stuart / Gunnar F Schröder / Joel C Watts /
Abstract: α-Synuclein conformational strains provide a potential explanation for the clinical and pathological differences among synucleinopathies such as Parkinson's disease and multiple system atrophy. ...α-Synuclein conformational strains provide a potential explanation for the clinical and pathological differences among synucleinopathies such as Parkinson's disease and multiple system atrophy. However, how distinct α-synuclein strains arise remains unknown. Here, we observed conformational heterogeneity between individual preparations of α-synuclein pre-formed fibrils (PFFs) generated by polymerizing wild-type or A53T-mutant human α-synuclein under identical conditions. Moreover, we found that α-synuclein aggregates formed spontaneously in the brains of a transgenic synucleinopathy mouse model are conformationally diverse. Propagation of stochastically formed PFF- and brain-derived α-synuclein strains in mice initiated several distinct synucleinopathies. The conformational diversity of α-synuclein aggregates across PFF preparations and between individual mice demonstrates that α-synuclein can spontaneously form multiple self-propagating strains within an identical environment. This suggests that stochastic misfolding into distinct aggregate structures drives the emergence of α-synuclein strains and reveals that the intrinsic variability of common synucleinopathy research tools must be considered when designing and interpreting experiments.
History
DepositionMay 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
F: Alpha-synuclein
G: Alpha-synuclein
H: Alpha-synuclein
I: Alpha-synuclein
J: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)145,06110
Polymers145,06110
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "E"
d_5ens_1chain "D"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 14 - 98 / Label seq-ID: 14 - 98

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3AA
d_4EE
d_5DD
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(-0.999991237735, 0.00418622188058, 8.23363751709E-8), (-0.00418622188053, -0.999991237735, 5.99366848414E-7), (8.4844736333E-8, 5.99016918268E-7, 1)261.156687296, 262.252204055, -2.46011154165
2given(0.999964947633, -0.00837278356407, 6.21652918632E-8), (0.00837278356407, 0.999964947633, -1.84937226575E-8), (-6.20082688855E-8, 1.90135709427E-8, 1)1.10018466928, -1.09105003535, -4.91999425327
3given(0.999964941082, 0.0083735659893, -9.86334102206E-8), (-0.00837356598935, 0.999964941082, -5.53928218849E-7), (9.3991597746E-8, 5.54734712094E-7, 1)-1.09112913803, 1.10038483767, 4.91989423558
4given(-0.999991240478, -0.00418556653113, -5.2055084174E-8), (0.00418556653113, -0.999991240478, 1.22521802395E-8), (-5.21059105119E-8, 1.20341928981E-8, 1)262.252160623, 261.156777564, 2.46000545881
5given(-0.999921139476, -0.0125584564789, 1.36505451334E-7), (0.0125584564789, -0.999921139476, 3.90490707147E-7), (1.31590725892E-7, 3.92174210615E-7, 1)263.338581103, 260.051912715, 7.37991487426
6given(0.999859801372, 0.0167444796729, 1.46325330581E-7), (-0.0167444796728, 0.999859801372, -3.17884324624E-7), (-1.51627623583E-7, 3.15389616155E-7, 1)-2.17276439225, 2.2094755479, 9.83996725722
7given(-0.999780954921, -0.0209294571408, -4.29453862631E-7), (0.0209294571404, -0.999780954921, 9.30934819974E-7), (-4.48843753292E-7, 9.21742667071E-7, 0.999999999999)264.41570265, 258.938138557, 12.29991251
8given(0.999684593799, 0.0251139985026, -1.23302683721E-7), (-0.0251139985027, 0.999684593799, -4.92184947973E-7), (1.10903061243E-7, 4.95126333203E-7, 1)-3.244970164, 3.32755277583, 14.7599013609
9given(-0.999570710773, -0.0292983645346, 2.14243406903E-9), (0.0292983645346, -0.999570710773, 3.72664950959E-7), (-8.77695923732E-9, 3.72567739725E-7, 1)265.483191739, 257.815650397, 17.2199378893

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Components

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


Mass: 14506.136 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37840
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: A53T alpha-synuclein fibril - Type 1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.79 ° / Axial rise/subunit: 2.49 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37465 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 89.73 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00185210
ELECTRON MICROSCOPYf_angle_d0.3817020
ELECTRON MICROSCOPYf_chiral_restr0.0466920
ELECTRON MICROSCOPYf_plane_restr0.0014870
ELECTRON MICROSCOPYf_dihedral_angle_d3.1378740
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints0.000567410193266
ens_1d_3CCELECTRON MICROSCOPYNCS constraints0.00054704639782
ens_1d_4CCELECTRON MICROSCOPYNCS constraints0.000564146922065
ens_1d_5CCELECTRON MICROSCOPYNCS constraints0.000557632063041
ens_1d_6CCELECTRON MICROSCOPYNCS constraints0.000556808761764
ens_1d_7CCELECTRON MICROSCOPYNCS constraints0.000578682982065
ens_1d_8CCELECTRON MICROSCOPYNCS constraints0.000568712177196
ens_1d_9CCELECTRON MICROSCOPYNCS constraints0.000547838577457
ens_1d_10CCELECTRON MICROSCOPYNCS constraints0.000575981673597

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