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- PDB-2kkw: SLAS-micelle bound alpha-synuclein -

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Basic information

Entry
Database: PDB / ID: 2kkw
TitleSLAS-micelle bound alpha-synuclein
ComponentsAlpha-synuclein
KeywordsLIPID BINDING PROTEIN / Protein-micelle interaction
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 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 / dopamine uptake involved in synaptic transmission / regulation of locomotion / synaptic vesicle priming / 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
Helix hairpin bin / Synuclein / Alpha-synuclein / Synuclein / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / EPR / simulated annealing
Model detailsmost populated ensemble subset representative, model 1
AuthorsRao, J. / Jao, C.C. / Hegde, B. / Langen, R. / Ulmer, T.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: A combinatorial NMR and EPR approach for evaluating the structural ensemble of partially folded proteins.
Authors: Rao, J.N. / Jao, C.C. / Hegde, B.G. / Langen, R. / Ulmer, T.S.
History
DepositionJun 29, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 13, 2019Group: Data collection / Category: pdbx_nmr_exptl / Item: _pdbx_nmr_exptl.conditions_id
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)14,4761
Polymers14,4761
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)34 / 85000ENSEMBLE SUBPOPULATION AVERAGE REPRESENTATIVES
RepresentativeModel #1

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCA, NACP, PARK1 / Plasmid: pET-42 / Production host: Escherichia coli (E. coli) / References: UniProt: P37840

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
EPR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TRIPLE RESONANCE
121QUANTITATIVE J CORRELATION HNCO
1314-PULSE DEER
NMR detailsText: EPR EXPERIMENT WAS DONE USING ELEXSYS E 580 SPECTROMETER AT 0.45 T, 78K, AMBIENT PRESSURE, PH 7.4, IONIC STRENGHT 0.1. THE EPR SAMPLE CONTAINED 50 UM ALPHA-SYNUCLEIN, 5 MM SODIUM LAUROYL SARCOSINATE, 30% SUCROSE

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Sample preparation

DetailsContents: 0.75 MM [U-100% 13C, U-100% 15N, U-80% 2H] ALPHA-SYNUCLEIN, 75 MM SODIUM LAUROYL SARCOSINATE, 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMentity-1[U-100% 13C; U-100% 15N; U-80% 2H]1
75 mMsodium lauroyl sarcosinate-21
50 uMentity-32
5 mMsodium lauroyl sarcosinate-42
30 %sucrose-52
Sample conditionsIonic strength: 0.05 / pH: 7.4 / Pressure: AMBIENT / Temperature: 298.2 K

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Data collection

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERS, KUSZEWSKI, TJrefinement
X-PLOR NIHstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: ENSEMBLE SUBPOPULATION AVERAGE REPRESENTATIVES
Conformers calculated total number: 85000 / Conformers submitted total number: 34

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