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- PDB-2n0a: Atomic-resolution structure of alpha-synuclein fibrils -

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Basic information

Entry
Database: PDB / ID: 2n0a
TitleAtomic-resolution structure of alpha-synuclein fibrils
ComponentsAlpha-synuclein
KeywordsSTRUCTURAL PROTEIN / Protein Fibril / Amyloid / Parkinson's Disease
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 macrophage activation / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / 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 / positive regulation of endocytosis / 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 / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / kinesin binding / alpha-tubulin binding / regulation of presynapse assembly / 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 / synapse organization / phospholipid binding / protein tetramerization / phosphoprotein binding / microglial cell activation / regulation of long-term neuronal synaptic plasticity / negative regulation of protein kinase activity / tau protein binding / protein destabilization / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / 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 / histone binding / growth cone / chemical synaptic transmission / postsynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide / lysosome / molecular adaptor activity / oxidoreductase activity / transcription cis-regulatory region binding
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsTuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Schwieters, C.D. / Lee, V.M. ...Tuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Schwieters, C.D. / Lee, V.M. / George, J.M. / Rienstra, C.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Solid-state NMR structure of a pathogenic fibril of full-length human alpha-synuclein.
Authors: Tuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Barclay, A.M. / Kendall, A. / Wan, W. / Stubbs, G. / Schwieters, ...Authors: Tuttle, M.D. / Comellas, G. / Nieuwkoop, A.J. / Covell, D.J. / Berthold, D.A. / Kloepper, K.D. / Courtney, J.M. / Kim, J.K. / Barclay, A.M. / Kendall, A. / Wan, W. / Stubbs, G. / Schwieters, C.D. / Lee, V.M. / George, J.M. / Rienstra, C.M.
History
DepositionMar 4, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jun 1, 2016Group: Structure summary
Revision 1.4Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name

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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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area108397.4 Å2
ΔGint30.2 kcal/mol
Surface area53490.2 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37840

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
Details: Atomic-resolution structure of alpha-synuclein fibrils
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
117Cross Polarization C1D
1213D NCACX
1313D NCOCX
1413D CANCO
1512D CC DARR
1622D CC DARR
1723D NCOCX
1822D NC TEDOR
1922D CC DARR
11022D CC DARR
11123D NCOCX
11232D CC DARR
11333D NCACX
11432D CC DARR
11532D NC TEDOR
11632D CC DARR
11733D NCACX
11842D NC TEDOR
11952D NC TEDOR
12062D CC DARR
12162D ChhC

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Sample preparation

Details
Solution-IDContentsSolvent system
166% [U-100% 13C; U-100% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
266% [U-100% 13C 1,3-Glycerol; U-100% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
366% [U-100% 13C 2-Glycerol; U-100% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
466% [U-25% 13C; U-25% 15N] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
566% [U-25% 13C 1,3-Glycerol; natural abundance N][natural abundance C13, U-50% N15] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
666% [U-25% 13C 2-Glycerol; natural abundance N][natural abundance C13, U-50% N15] alpha-synuclein, 34% H2O, Rehydrated FibrilRehydrated Fibril
790% Adamantane, 10% KBr, DryDry
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
66 %alpha-synuclein-1[U-100% 13C; U-100% 15N]1
34 %H2O-21
66 %alpha-synuclein-3[U-100% 13C 1,3-Glycerol; U-100% 15N]2
34 %H2O-42
66 %alpha-synuclein-5[U-100% 13C 2-Glycerol; U-100% 15N]3
34 %H2O-63
66 %alpha-synuclein-7[U-25% 13C; U-25% 15N]4
34 %H2O-84
66 %alpha-synuclein-9[U-25% 13C 1,3-Glycerol; natural abundance N][natural abundance C13, U-50% N15]5
34 %H2O-105
66 %alpha-synuclein-11[U-25% 13C 2-Glycerol; natural abundance N][natural abundance C13, U-50% N15]6
34 %H2O-126
90 %Adamantane-137
10 %KBr-147
Sample conditionspH: 7 / Pressure: ambient / Temperature units: K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent VNMRSAgilentVNMRS7501
Agilent InfinityPlusAgilentInfinityPlus6002
Agilent VNMRSAgilentVNMRS5003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.33.4Schwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIH2.33.4Schwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIH2.33.4Schwieters, Kuszewski, Tjandra and Clorestructure solution
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 450 / Protein psi angle constraints total count: 450
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 256 / Conformers submitted total number: 1 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0 Å / Representative conformer: 1 / Torsion angle constraint violation method: Degrees
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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