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- PDB-8cyy: CryoEM structure of amplified alpha-synuclein fibril class B mixe... -

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Basic information

Entry
Database: PDB / ID: 8cyy
TitleCryoEM structure of amplified alpha-synuclein fibril class B mixed type I/II with extended core from DLB case V
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / alpha-synuclein / Cerebrospinal Fluid (CSF) / DLB
Function / homology
Function and homology information


regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process ...regulation of phospholipase activity / negative regulation of monooxygenase activity / negative regulation of mitochondrial electron transport, NADH to ubiquinone / positive regulation of glutathione peroxidase activity / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / 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 reactive oxygen species biosynthetic process / regulation of synaptic vesicle recycling / 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 / 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 / response to type II interferon / synaptic vesicle exocytosis / positive regulation of exocytosis / kinesin binding / positive regulation of endocytosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitochondrial ATP synthesis coupled electron transport / response to magnesium ion / synaptic vesicle endocytosis / regulation of presynapse assembly / negative regulation of serotonin uptake / alpha-tubulin binding / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / : / adult locomotory behavior / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / excitatory postsynaptic potential / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / negative regulation of protein kinase activity / microglial cell activation / synapse organization / regulation of long-term neuronal synaptic plasticity / protein destabilization / ferrous iron binding / tau protein binding / positive regulation of protein serine/threonine kinase activity / PKR-mediated signaling / receptor internalization / phospholipid binding / : / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / actin binding / cellular response to oxidative stress / histone binding / cell cortex / growth cone / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynapse / amyloid fibril formation / response to lipopolysaccharide / molecular adaptor activity / lysosome / oxidoreductase activity / 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
C: Alpha-synuclein
K: Alpha-synuclein
A: Alpha-synuclein
I: Alpha-synuclein
B: Alpha-synuclein
J: Alpha-synuclein
D: Alpha-synuclein
L: Alpha-synuclein
E: Alpha-synuclein
M: Alpha-synuclein
F: Alpha-synuclein
N: 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "E"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "A"
d_6ens_1chain "F"
d_1ens_2chain "K"
d_2ens_2chain "J"
d_3ens_2chain "I"
d_4ens_2chain "L"
d_5ens_2chain "M"
d_6ens_2chain "N"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1VALLYSI1 - 72
d_21ens_1VALLYSE1 - 72
d_31ens_1VALLYSA1 - 72
d_41ens_1VALLYSG1 - 72
d_51ens_1VALLYSC1 - 72
d_61ens_1VALLYSK1 - 72
d_11ens_2VALLYSB1 - 72
d_21ens_2VALLYSF1 - 72
d_31ens_2VALLYSD1 - 72
d_41ens_2VALLYSH1 - 72
d_51ens_2VALLYSJ1 - 72
d_61ens_2VALLYSL1 - 72

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.999925378281, -0.0122162348189, 3.84323718547E-5), (0.0122162349749, 0.99992537901, -3.82586968841E-6), (-3.83827662706E-5, 4.29508308066E-6, 0.999999999254)0.798461682244, -0.790907631639, -4.83775715579
2given(0.99970149704, -0.0244317645815, 7.54631114424E-5), (0.0244317653274, 0.99970149983, -8.97762961144E-6), (-7.52212463576E-5, 1.08186467921E-5, 0.999999997112)1.60660179435, -1.57228156571, -9.67581545811
3given(0.999925365406, 0.0122172957757, -3.60758932585E-5), (-0.0122172955536, 0.999925366039, 6.36830149541E-6), (3.61510041947E-5, -5.92707634951E-6, 0.999999999329)-0.789347269333, 0.801257395366, 4.8380981523
4given(0.999701435787, 0.0244342757898, -7.38433702316E-5), (-0.0244342751179, 0.99970143848, 9.98723317036E-6), (7.40653542525E-5, -8.17994211606E-6, 0.999999997224)-1.56900216753, 1.61209554332, 9.6757385056
5given(0.999328391184, 0.0366436184605, -0.000108626605682), (-0.0366436167454, 0.999328396993, 1.77382435841E-5), (0.000109203645157, -1.37458587164E-5, 0.999999993943)-2.33863431302, 2.43185907167, 14.5138963312
6given(0.99992539292, -0.0122150511167, 3.34535432725E-5), (0.012215051294, 0.999925393465, -5.10029031917E-6), (-3.33887471126E-5, 5.50854654844E-6, 0.999999999427)0.798804809542, -0.791116396873, -4.8381265698
7given(0.999925357686, 0.0122179175358, -3.93395741884E-5), (-0.0122179173738, 0.999925358452, 4.35563546923E-6), (3.93898546166E-5, -3.87466268757E-6, 0.999999999217)-0.78892629437, 0.800704158978, 4.83779619251
8given(0.999701469283, 0.024432898884, -7.59310535837E-5), (-0.0244328981473, 0.999701472128, 1.06155390463E-5), (7.61677544399E-5, -8.75715428342E-6, 0.999999997061)-1.56861439766, 1.61155604052, 9.67572728329
9given(0.999328353674, 0.0366446253441, -0.000113911347582), (-0.0366446236851, 0.999328360089, 1.66178277676E-5), (0.000114443794247, -1.24324279991E-5, 0.999999993374)-2.33826712647, 2.43165478371, 14.5135102758
10given(0.998806150603, 0.0488492712269, -0.000149058007479), (-0.0488492683673, 0.998806161606, 2.27675798095E-5), (0.000149992235988, -1.54590241385E-5, 0.999999988632)-3.09811488087, 3.26102151496, 19.3513703169

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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) / 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
NameVersionClassification
phenix.real_space_refine1.20_4459refinement
PHENIX1.20_4459refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.71 ° / Axial rise/subunit: 4.8 Å / Axial symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164382 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 31.05 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055976
ELECTRON MICROSCOPYf_angle_d0.95488052
ELECTRON MICROSCOPYf_chiral_restr0.06611068
ELECTRON MICROSCOPYf_plane_restr0.0038984
ELECTRON MICROSCOPYf_dihedral_angle_d7.85572040
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2IELECTRON MICROSCOPYNCS constraints5.12314228864E-12
ens_1d_3IELECTRON MICROSCOPYNCS constraints3.73195748281E-12
ens_1d_4IELECTRON MICROSCOPYNCS constraints1.15406089579E-12
ens_1d_5IELECTRON MICROSCOPYNCS constraints7.92143267781E-12
ens_1d_6IELECTRON MICROSCOPYNCS constraints1.13852664966E-12
ens_2d_2BELECTRON MICROSCOPYNCS constraints1.17928176156E-12
ens_2d_3BELECTRON MICROSCOPYNCS constraints5.20515468961E-12
ens_2d_4BELECTRON MICROSCOPYNCS constraints1.188467327E-12
ens_2d_5BELECTRON MICROSCOPYNCS constraints5.59890653646E-12
ens_2d_6BELECTRON MICROSCOPYNCS constraints8.3516737315E-12

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