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- PDB-8fpt: STRUCTURE OF ALPHA-SYNUCLEIN FIBRILS DERIVED FROM HUMAN LEWY BODY... -

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Basic information

Entry
Database: PDB / ID: 8fpt
TitleSTRUCTURE OF ALPHA-SYNUCLEIN FIBRILS DERIVED FROM HUMAN LEWY BODY DEMENTIA TISSUE
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / AMYLOID / LEWY BODY DEMENTIA / POLYMORPHISM / PARKINSON / STRUCTURAL PROTEIN
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 / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / response to iron(II) ion / regulation of norepinephrine uptake / dopamine biosynthetic process / SNARE complex assembly / positive regulation of neurotransmitter secretion / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / regulation of macrophage activation / mitochondrial ATP synthesis coupled electron transport / negative regulation of microtubule polymerization / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / kinesin binding / regulation of presynapse assembly / alpha-tubulin binding / synaptic vesicle endocytosis / negative regulation of serotonin uptake / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / Hsp70 protein binding / cellular response to epinephrine stimulus / excitatory postsynaptic potential / response to interleukin-1 / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / regulation of transmembrane transporter activity / ferrous iron binding / protein tetramerization / synapse organization / phosphoprotein binding / regulation of long-term neuronal synaptic plasticity / microglial cell activation / negative regulation of protein kinase activity / phospholipid binding / protein destabilization / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / tau protein binding / positive regulation of protein serine/threonine kinase activity / receptor internalization / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin cytoskeleton / positive regulation of peptidyl-serine phosphorylation / cellular response to oxidative stress / actin binding / cell cortex / growth cone / histone binding / chemical synaptic transmission / postsynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / lysosome / oxidoreductase activity / molecular adaptor activity / transcription cis-regulatory region binding
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsBarclay, A.M. / Dhavale, D.D. / Borcik, C.G. / Rau, M.J. / Basore, K. / Milchberg, M.H. / Warmuth, O.A. / Kotzbauer, P.T. / Rienstra, C.M. / Schwieters, C.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biorxiv / Year: 2023
Title: Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue.
Authors: Dhavale, D.D. / Barclay, A.M. / Borcik, C.G. / Basore, K. / Gordon, I.R. / Liu, J. / Milchberg, M.H. / Oa Shea, J. / Rau, M.J. / Smith, Z. / Sen, S. / Summers, B. / Smith, J. / Warmuth, O.A. ...Authors: Dhavale, D.D. / Barclay, A.M. / Borcik, C.G. / Basore, K. / Gordon, I.R. / Liu, J. / Milchberg, M.H. / Oa Shea, J. / Rau, M.J. / Smith, Z. / Sen, S. / Summers, B. / Smith, J. / Warmuth, O.A. / Chen, Q. / Fitzpatrick, J.A.J. / Schwieters, C.D. / Tajkhorshid, E. / Rienstra, C.M. / Kotzbauer, P.T.
History
DepositionJan 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 256structures with the lowest energy
RepresentativeModel #1lowest energy

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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 / Plasmid: PET28A-AS / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): HUMAN BRAIN TISSUE / References: UniProt: P37840

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D CC DARR
1301isotropic12D CC SPC7
1291isotropic13D NCACX DARR
1281isotropic13D NCOCX DARR
1271isotropic13D CANCO
1261isotropic22D CC DARR
1251isotropic22D NCA
1241isotropic22D NCO
1231isotropic23D NCACX DARR
1221isotropic23D NCOCX DARR
1211isotropic23D NCOCA SPC5
1201isotropic23D CANCO
1191isotropic12D CC PAR
1181isotropic13D CCC RFDR THEN PAR
1171isotropic23D NCACX PAR
1161isotropic21D C FSREDOR
1152isotropic13D CANH
1142isotropic13D CONH
1132isotropic13D CA[CO]NH RFDR
1122isotropic13D CO[CA]NH RFDR
1112isotropic13D CAN[H]H RFDR
1102isotropic13D CA[HH]NH RFDR
192isotropic13D N[HH]NH RFDR
182isotropic14D HN[HH]NH RFDR
172isotropic12D CACO CTUC-COSY
162isotropic22D CC FPRFDR
153isotropic22D CC DARR
143isotropic22D NCA
133isotropic22D NCO

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid166 % [U-100% 13C; U-100% 15N] ALPHA-SYNUCLEIN, 34% H2OREHYDRATED FIBRILuCN34% H2O
solid266 % [U-100% 2H; U-100% 13C; U-100% 15N] ALPHA-SYNUCLEIN, 34% H2O, BACK-EXCHANGED IN 99.8% D2OuDCN34% H2O, BACK-EXCHANGED IN 99.8% D2O
solid320 % [U-25% 2-13C GLYCEROL; U-100% 15N] labelled ALPHA-SYNUCLEIN, 80 % ALPHA-SYNUCLEIN, H2ODilutedH2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
66 %ALPHA-SYNUCLEIN[U-100% 13C; U-100% 15N]1
66 %ALPHA-SYNUCLEIN[U-100% 2H; U-100% 13C; U-100% 15N]2
20 %labelled ALPHA-SYNUCLEIN[U-25% 2-13C GLYCEROL; U-100% 15N]3
80 %ALPHA-SYNUCLEINnatural abundance3
Sample conditionsIonic strength: 100 mM NACL mM / Label: SAMPLE_COND / pH: 7.6 / Pressure: AMBIENT / Temperature: 273 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent VNMRSAgilentVNMRS7501
Agilent VNMRSAgilentVNMRS5002

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRFAM-SPARKYLEE, TONELLI and MARKLEYchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRFAM-SPARKYLEE, TONELLI, and MARKLEYpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 256 / Conformers submitted total number: 10

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