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- PDB-9rb9: Wild-type alpha-synuclein fibril - Type 3-2 -

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Basic information

Entry
Database: PDB / ID: 9rb9
TitleWild-type alpha-synuclein fibril - Type 3-2
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: 3.04 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
C: Alpha-synuclein
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


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: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 37 - 80 / Label seq-ID: 37 - 80

Dom-IDAuth asym-IDLabel asym-ID
d_1AB
d_2BC
d_3CA
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(0.999779420237, 0.0207509278171, 0.00324189221889), (-0.0207503431942, 0.999784665574, -0.000213868784658), (-0.0032456321036, 0.000146551233392, 0.999994722184)-2.97670129889, 2.74552562155, 5.24894932666
2given(0.998955612973, 0.0456909835585, 0.000131649304672), (-0.0456902349479, 0.998949417775, -0.00353031964561), (-0.000292814773137, 0.00352061753791, 0.999993759736)-5.76010775746, 6.49296536626, 9.14950637125
3given(0.997401747679, 0.0720020032852, 0.00233778754996), (-0.0719993368175, 0.997403951395, -0.00120550372044), (-0.00241851722269, 0.00103405236438, 0.999996540749)-9.1742856095, 9.79134052149, 14.55163252
4given(0.994831875672, 0.101534639501, 0.000506091207934), (-0.101534806697, 0.994831937039, 0.000316348145023), (-0.000471355401846, -0.000366099091448, 0.999999821898)-12.502023703, 13.7247743722, 19.2876535405
5given(-0.999999792484, 0.000560890483707, -0.000316913160959), (-0.000561082700513, -0.999999658511, 0.000606765303382), (-0.000316572723852, 0.000606942991961, 0.999999765701)258.515719984, 258.555987798, -0.0227607323718
6given(-0.999667135878, -0.0257953953766, -0.000463704594787), (0.0257950983237, -0.999667049052, 0.000635564585606), (-0.000479944843676, 0.000623391723343, 0.999999690518)261.902289313, 255.093387532, 4.77952398783
7given(-0.998660777632, -0.0517363059809, -7.65695285931E-5), (0.0517362286725, -0.998660465971, 0.000797715443295), (-0.000117737811364, 0.000792685706289, 0.999999678894)265.083538744, 251.602779712, 9.49103665974
8given(-0.997079343115, -0.0763726610096, -1.35671061957E-5), (0.0763725399356, -0.99707804886, 0.00161233511879), (-0.000136665787235, 0.00160658988676, 0.999998700095)268.016673916, 248.123401252, 14.1750721715
9given(-0.994608328383, -0.103702407491, 0.000289466361145), (0.103702664364, -0.994607744476, 0.00109180234133), (0.00017468295326, 0.00111593413453, 0.999999362088)271.238225362, 244.314986086, 18.9830094988

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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 3-2 / 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: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.5 ° / Axial rise/subunit: 4.79 Å / Axial symmetry: C2
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20107 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 75.88 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02263110
ELECTRON MICROSCOPYf_angle_d2.74314220
ELECTRON MICROSCOPYf_chiral_restr0.1287570
ELECTRON MICROSCOPYf_plane_restr0.0097520
ELECTRON MICROSCOPYf_dihedral_angle_d10.66831070
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAELECTRON MICROSCOPYNCS constraints0.000704954965282
ens_1d_3BAELECTRON MICROSCOPYNCS constraints0.000522542694644
ens_1d_4BAELECTRON MICROSCOPYNCS constraints0.000736764588315
ens_1d_5BAELECTRON MICROSCOPYNCS constraints0.000710489152812
ens_1d_6BAELECTRON MICROSCOPYNCS constraints0.000712170968672
ens_1d_7BAELECTRON MICROSCOPYNCS constraints0.000699420781858
ens_1d_8BAELECTRON MICROSCOPYNCS constraints0.000691861013637
ens_1d_9BAELECTRON MICROSCOPYNCS constraints0.000718308106236
ens_1d_10BAELECTRON MICROSCOPYNCS constraints0.000712056056254

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