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- PDB-8ojr: Solution NMR Structure of Alpha-Synuclein 1-25 Peptide in 50% TFE. -

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Basic information

Entry
Database: PDB / ID: 8ojr
TitleSolution NMR Structure of Alpha-Synuclein 1-25 Peptide in 50% TFE.
ComponentsAlpha-synuclein
KeywordsLIPID BINDING PROTEIN / inhibitor
Function / homology
Function and homology information


regulation of dopamine secretion / axon / synapse / extracellular region / membrane / nucleus / cytoplasm
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsAllen, S.G. / Williams, C. / Meade, R.M. / Tang, T.M.S. / Crump, M.P. / Mason, J.M.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/1 United Kingdom
Alzheimers Research UK (ARUK)ARUK-PG2018-003 United Kingdom
Engineering and Physical Sciences Research CouncilEP/L016354/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L01386X/1 United Kingdom
CitationJournal: Cell Rep Phys Sci / Year: 2023
Title: An N-terminal alpha-Synuclein fragment binds lipid vesicles to modulate lipid induced aggregation
Authors: Meade, R.M. / Allen, S.G. / Williams, C. / Tang, T.M.S. / Crump, M.P. / Mason, J.M.
History
DepositionMar 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)2,6531
Polymers2,6531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry, Mass was that of capped peptide.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area2570 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Alpha-synuclein /


Mass: 2653.168 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Synthetic peptide with N-terminal acetyl and C-terminal amide caps
Source: (synth.) Homo sapiens (human) / References: UniProt: H6UYS7
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-13C HSQC
131isotropic12D 1H-1H TOCSY
141isotropic12D 1H-1H COSY
151isotropic12D 1H-15N HSQC
161isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

DetailsType: solution
Contents: 1 mM aSyn_1-25, 20 mM potassium phosphate, 10 % [U-100% 2H] D2O, 50 % [U-2H] 2,2,2-Trifluoroethanol, trifluoroethanol/water
Details: Peptide dissolved in 20mM potassium phosphate buffer with 10% D2O with TFE-d2 added to 50%
Label: aSyn Peptide / Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMaSyn_1-25natural abundance1
20 mMpotassium phosphatenatural abundance1
10 %D2O[U-100% 2H]1
50 %2,2,2-Trifluoroethanol[U-2H]1
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz / Details: TXO cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
DANGLE1.1Cheung MS, Maguire ML, Stevens TJ, Broadhurst RWdata analysis
ARIA2.3.2Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
AnalysisAssign2.5.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpin4.1.3Bruker Biospincollection
TopSpin4.1.3Bruker Biospinprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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