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- PDB-9o9k: Cryo-EM structure of alpha-synuclein filaments from Parkinson's d... -

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Basic information

Entry
Database: PDB / ID: 9o9k
TitleCryo-EM structure of alpha-synuclein filaments from Parkinson's disease with H50Q variant in SNCA
Components
  • Alpha-synuclein
  • unassigned chain
KeywordsPROTEIN FIBRIL / amyloid / filament / synuclein / human brain / cryo-EM / fibril / PD / H50Q / mutation
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 / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / mitochondrial membrane organization / negative regulation of exocytosis / regulation of glutamate secretion / dopamine biosynthetic process / response to iron(II) ion / positive regulation of neurotransmitter secretion / regulation of macrophage activation / negative regulation of dopamine metabolic process / negative regulation of platelet-derived growth factor receptor signaling pathway / SNARE complex assembly / negative regulation of thrombin-activated receptor signaling pathway / Lewy body / regulation of locomotion / negative regulation of microtubule polymerization / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of norepinephrine uptake / transporter regulator activity / protein kinase inhibitor activity / synaptic vesicle transport / dopamine uptake involved in synaptic transmission / regulation of dopamine secretion / positive regulation of receptor recycling / positive regulation of exocytosis / cuprous ion binding / nuclear outer membrane / mitochondrial ATP synthesis coupled electron transport / dynein complex binding / synaptic vesicle exocytosis / response to magnesium ion / positive regulation of endocytosis / negative regulation of serotonin uptake / response to type II interferon / cysteine-type endopeptidase inhibitor activity / kinesin binding / regulation of presynapse assembly / synaptic vesicle endocytosis / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / phospholipid metabolic process / supramolecular fiber organization / behavioral response to cocaine / cellular response to fibroblast growth factor stimulus / cellular response to epinephrine stimulus / inclusion body / Hsp70 protein binding / enzyme inhibitor activity / response to interleukin-1 / axon terminus / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / regulation of microtubule cytoskeleton organization / SNARE binding / adult locomotory behavior / glutathione metabolic process / protein tetramerization / protein sequestering activity / tubulin binding / phosphoprotein binding / excitatory postsynaptic potential / microglial cell activation / ferrous iron binding / fatty acid metabolic process / PKR-mediated signaling / phospholipid binding / synapse organization / receptor internalization / regulation of long-term neuronal synaptic plasticity / 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 / cellular response to oxidative stress / neuron apoptotic process / 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
RNA / Alpha-synuclein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYang, Y. / Murzin, G.A. / Scheres, H.W.S. / Goedert, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105184291 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1013 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of alpha-synuclein filaments from Parkinson's disease with H50Q variant in SNCA
Authors: Yang, Y. / Murzin, G.A. / Scheres, H.W.S. / Goedert, M.
History
DepositionApr 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 20, 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

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Assembly

Deposited unit
A: Alpha-synuclein
B: unassigned chain
C: unassigned chain


Theoretical massNumber of molelcules
Total (without water)15,9083
Polymers15,9083
Non-polymers00
Water18010
1
A: Alpha-synuclein
B: unassigned chain
C: unassigned chain
x 5


Theoretical massNumber of molelcules
Total (without water)79,54015
Polymers79,54015
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
point symmetry operation1_555x,y,z1
point symmetry operation3
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.999519, 0.031001), (-0.031001, 0.999519), (1)-3.0072, 3.1019, -9.4539
3generate(0.99988, 0.015502), (-0.015502, 0.99988), (1)-1.5156, 1.5393, -4.727
4generate(0.99988, -0.015502), (0.015502, 0.99988), (1)1.5393, -1.5156, 4.727
5generate(0.999519, -0.031001), (0.031001, 0.999519), (1)3.1019, -3.0072, 9.4539

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Components

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


Mass: 14466.091 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P37840
#2: RNA chain unassigned chain


Mass: 720.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
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 filaments extracted from the human Parkinson's disease brain with H50Q variant in SNCA
Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 2600 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0.89 ° / Axial rise/subunit: 4.73 Å / Axial symmetry: C1
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200126 / Symmetry type: HELICAL
RefinementResolution: 2.9→96.34 Å / Cor.coef. Fo:Fc: 0.785 / SU B: 13.248 / SU ML: 0.243 / ESU R: 0.175
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.4082 --
obs0.4082 28748 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 58.006 Å2
Refinement stepCycle: 1 / Total: 577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.012566
ELECTRON MICROSCOPYr_bond_other_d00.016591
ELECTRON MICROSCOPYr_angle_refined_deg1.5431.786763
ELECTRON MICROSCOPYr_angle_other_deg0.5331.7411352
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.515583
ELECTRON MICROSCOPYr_dihedral_angle_2_deg
ELECTRON MICROSCOPYr_dihedral_angle_3_deg9.1691089
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0550.2101
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02650
ELECTRON MICROSCOPYr_gen_planes_other0.0020.02102
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.1695.024341
ELECTRON MICROSCOPYr_mcbond_other6.1685.022341
ELECTRON MICROSCOPYr_mcangle_it9.3358.96421
ELECTRON MICROSCOPYr_mcangle_other9.3338.973422
ELECTRON MICROSCOPYr_scbond_it9.8276.381225
ELECTRON MICROSCOPYr_scbond_other9.8066.392226
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other16.03910.93343
ELECTRON MICROSCOPYr_long_range_B_refined19.25749.75545
ELECTRON MICROSCOPYr_long_range_B_other19.25149.78545
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.885 2054 -
obs--100 %

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