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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 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 / mitochondrial membrane organization ...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 / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / 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 / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of norepinephrine uptake / transporter regulator activity / regulation of locomotion / synaptic vesicle priming / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / dynein complex binding / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / positive regulation of endocytosis / positive regulation of exocytosis / response to magnesium ion / synaptic vesicle exocytosis / enzyme inhibitor activity / kinesin binding / synaptic vesicle endocytosis / regulation of presynapse assembly / response to type II interferon / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / alpha-tubulin binding / supramolecular fiber organization / inclusion body / phospholipid metabolic process / cellular response to copper ion / axon terminus / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / negative regulation of protein kinase activity / excitatory postsynaptic potential / fatty acid metabolic process / phosphoprotein binding / protein tetramerization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / actin binding / growth cone / cell cortex / cellular response to oxidative stress / neuron apoptotic process / chemical synaptic transmission / molecular adaptor activity / negative regulation of neuron apoptotic process / response to lipopolysaccharide / histone binding / amyloid fibril formation / lysosome / oxidoreductase activity / postsynapse / transcription cis-regulatory region binding / positive regulation of apoptotic process / Amyloid fiber formation / copper ion binding / response to xenobiotic stimulus / axon / neuronal cell body
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: Nat Commun / Year: 2024
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. / Berthold, D.A. / Gordon, I.R. / Liu, J. / Milchberg, M.H. / O'Shea, J.Y. / Rau, M.J. / Smith, Z. / Sen, S. / Summers, B. / Smith, ...Authors: Dhavale, D.D. / Barclay, A.M. / Borcik, C.G. / Basore, K. / Berthold, D.A. / Gordon, I.R. / Liu, J. / Milchberg, M.H. / O'Shea, J.Y. / Rau, M.J. / Smith, Z. / Sen, S. / Summers, B. / Smith, J. / Warmuth, O.A. / Perrin, R.J. / Perlmutter, J.S. / 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
Revision 1.2Dec 11, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_nmr_spectrometer
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _pdbx_nmr_spectrometer.manufacturer

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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
Water00
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
Has protein modificationN

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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
Varian VNMRSVarianVNMRS7501
Varian VNMRSVarianVNMRS5002

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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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