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- PDB-8cyw: CryoEM structures of amplified alpha-synuclein fibril class B typ... -

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Basic information

Entry
Database: PDB / ID: 8cyw
TitleCryoEM structures of amplified alpha-synuclein fibril class B type I with compact core from DLB case III
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / Cerebrospinal Fluid (CSF)
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of synaptic vesicle recycling / regulation of reactive oxygen species biosynthetic process / 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 norepinephrine uptake / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / dopamine uptake involved in synaptic transmission / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / positive regulation of endocytosis / synaptic vesicle exocytosis / positive regulation of exocytosis / kinesin binding / response to magnesium ion / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / regulation of presynapse assembly / response to type II interferon / negative regulation of serotonin uptake / synaptic vesicle endocytosis / alpha-tubulin binding / supramolecular fiber organization / axon terminus / cellular response to copper ion / inclusion body / cellular response to epinephrine stimulus / phospholipid metabolic process / Hsp70 protein binding / response to interleukin-1 / : / SNARE binding / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / excitatory postsynaptic potential / fatty acid metabolic process / positive regulation of protein serine/threonine kinase activity / phosphoprotein binding / protein tetramerization / long-term synaptic potentiation / negative regulation of protein kinase activity / microglial cell activation / regulation of long-term neuronal synaptic plasticity / regulation of transmembrane transporter activity / synapse organization / tau protein binding / ferrous iron binding / : / PKR-mediated signaling / protein destabilization / receptor internalization / phospholipid binding / positive regulation of peptidyl-serine phosphorylation / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / actin binding / cellular response to oxidative stress / histone binding / growth cone / cell cortex / chemical synaptic transmission / neuron apoptotic process / molecular adaptor activity / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / oxidoreductase activity / lysosome / postsynapse / transcription cis-regulatory region binding / positive regulation of apoptotic process
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhou, Y. / Sokratian, A. / Xu, E. / Viverette, E. / Dillard, L. / Yuan, Y. / Li, J.Y. / Matarangas, A. / Bouvette, J. / Borgnia, M. ...Zhou, Y. / Sokratian, A. / Xu, E. / Viverette, E. / Dillard, L. / Yuan, Y. / Li, J.Y. / Matarangas, A. / Bouvette, J. / Borgnia, M. / Bartesaghi, A. / West, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Michael J. Fox Foundation United States
CitationJournal: To Be Published
Title: Structural and functional landscape of alpha-synuclein fibril assemblies amplified from cerebrospinal fluid
Authors: Zhou, Y. / Sokratian, A. / Xu, E. / Viverette, E. / Dillard, L. / Yuan, Y. / Li, J.Y. / Matarangas, A. / Bouvette, J. / Borgnia, M. / Bartesaghi, A. / West, A.
History
DepositionMay 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-synuclein
D: Alpha-synuclein
C: Alpha-synuclein
B: Alpha-synuclein
L: Alpha-synuclein
K: Alpha-synuclein
J: Alpha-synuclein
I: Alpha-synuclein
F: Alpha-synuclein
E: Alpha-synuclein
N: Alpha-synuclein
M: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)173,71312
Polymers173,71312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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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.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: cerebrospinal fluid / Gene: SNCA, NACP, PARK1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P37840

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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: Amplified alpha-synuclein fibrils from Lewy body dementia CSF
Type: ORGANELLE OR CELLULAR COMPONENT
Details: alpha-synuclein fibril produced in presence of postmortem cerebrospinal fluid from specimens affected by synucleinopathies
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 60 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Tissue: cerebrospinal fluid
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Plasmid: pRK172
Buffer solutionpH: 7.4 / Details: Gibco Cat # 10010072
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMSodium chlorideNaCl1
22.7 mMPotassium chlorideKCl1
310 mMDisodium phosphateNa2HPO41
41.8 mMMonopotassium phosphateKH2PO41
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 %

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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: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20_4459refinement
PHENIX1.20_4459refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.63 ° / Axial rise/subunit: 2.4 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14789 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 69.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00615964
ELECTRON MICROSCOPYf_angle_d1.09378040
ELECTRON MICROSCOPYf_chiral_restr0.05941056
ELECTRON MICROSCOPYf_plane_restr0.0049996
ELECTRON MICROSCOPYf_dihedral_angle_d7.1755864

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