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- PDB-9rbb: Wild-type alpha-synuclein fibril - Type 5 -

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Basic information

Entry
Database: PDB / ID: 9rbb
TitleWild-type alpha-synuclein fibril - Type 5
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / fibril
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: 3.15 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)144,76110
Polymers144,76110
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 "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
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: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 44 - 90 / Label seq-ID: 44 - 90

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(-0.999953502237, -0.00964330670816, 1.0400362502E-7), (0.00964330670818, -0.999953502237, 1.99886865669E-7), (1.02071218732E-7, 2.00880510232E-7, 1)247.180651876, 244.808261928, 2.38996244635
2given(0.999809990275, 0.0194815551239, -0.000672574900521), (-0.0194815622103, 0.99981021635, -3.98568188221E-6), (0.00067236960952, 1.70877343294E-5, 0.999999773814)-2.32485333611, 2.40985879423, 4.71100004341
3given(-0.999605031411, -0.028102317187, -0.000202354402908), (0.0281016528299, -0.999601264021, 0.00275863659088), (-0.000279797797408, 0.0027518605229, 0.999996174481)249.436038026, 242.209496027, 6.86704121684
4given(0.999265986413, 0.0383010805831, -0.000718070350104), (-0.0383010846551, 0.999266244226, 8.08493653794E-6), (0.000717853123644, 1.94238711829E-5, 0.999999742155)-4.55851286701, 4.80745418248, 9.48498292264
5given(-0.998887209912, -0.0471627295611, -0.000137164827586), (0.0471627696511, -0.998887170745, -0.000305418363193), (-0.000122607822887, -0.000311547569834, 0.999999943953)251.653987659, 240.086002739, 12.0085514179
6given(0.998331566731, 0.057740324492, 0.000371210116488), (-0.057740444324, 0.998331577326, 0.000320627603624), (-0.000352077639239, -0.000341526494927, 0.9999998797)-6.9377765453, 7.27743066126, 14.4150387043
7given(-0.99781086664, -0.0661171185404, 0.00141458544337), (0.0661166439664, -0.997811828558, -0.000379711541214), (0.00143659552088, -0.000285352659892, 0.999998927383)253.704383003, 237.61715267, 16.6078209221
8given(0.997032455348, 0.0769823550105, 2.7013468457E-7), (-0.0769823550104, 0.997032455348, -6.6728492575E-7), (-3.20702212879E-7, 6.44509123749E-7, 1)-9.1039753546, 9.83383162513, 19.119946757
9given(-0.99624506411, -0.0865781279334, -7.24142287965E-7), (0.0865781279327, -0.99624506411, 8.49754275523E-7), (-7.94993314476E-7, 7.83868619047E-7, 0.999999999999)256.187379676, 234.888969482, 21.509979916

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Components

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


Mass: 14476.108 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: Wild-type alpha-synuclein fibril - Type 5 / 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: 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: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.45 ° / Axial rise/subunit: 2.39 Å / Axial symmetry: C1
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38375 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 82.78 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02223160
ELECTRON MICROSCOPYf_angle_d2.38964290
ELECTRON MICROSCOPYf_chiral_restr0.1059590
ELECTRON MICROSCOPYf_plane_restr0.0076540
ELECTRON MICROSCOPYf_dihedral_angle_d15.97431050
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.000569885736164
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.000723149561349
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.000717163937979
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.000724093990647
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.000700476921372
ens_1d_7AAELECTRON MICROSCOPYNCS constraints0.000716270859612
ens_1d_8AAELECTRON MICROSCOPYNCS constraints0.000729835476268
ens_1d_9AAELECTRON MICROSCOPYNCS constraints0.000584283961923
ens_1d_10AAELECTRON MICROSCOPYNCS constraints0.000586586467511

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