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- PDB-2kes: Solution Structure of the Coiled-coil Domain of Synphilin-1 -

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Basic information

Entry
Database: PDB / ID: 2kes
TitleSolution Structure of the Coiled-coil Domain of Synphilin-1
ComponentsSynphilin-1
KeywordsPROTEIN BINDING / Synphillin / coiled-coil / ANK repeat / Disease mutation / Parkinson disease / Phosphoprotein / Polymorphism / Ubl conjugation
Function / homology
Function and homology information


regulation of inclusion body assembly / protein metabolic process => GO:0019538 / cell death / regulation of neurotransmitter secretion / dopamine metabolic process / cytoplasmic ribonucleoprotein granule / synaptic vesicle / presynaptic membrane / Amyloid fiber formation / neuronal cell body ...regulation of inclusion body assembly / protein metabolic process => GO:0019538 / cell death / regulation of neurotransmitter secretion / dopamine metabolic process / cytoplasmic ribonucleoprotein granule / synaptic vesicle / presynaptic membrane / Amyloid fiber formation / neuronal cell body / ubiquitin protein ligase binding / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #750 / Synphilin-1, alpha-Synuclein-binding domain / Synphilin-1 / Synphilin-1 alpha-Synuclein-binding domain / Domain of unknown function DUF3447 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #750 / Synphilin-1, alpha-Synuclein-binding domain / Synphilin-1 / Synphilin-1 alpha-Synuclein-binding domain / Domain of unknown function DUF3447 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsXie, Y.Y. / Zhou, C.J. / Zhou, Z.R. / Hu, H.Y.
CitationJournal: Faseb J. / Year: 2010
Title: Interaction with synphilin-1 promotes inclusion formation of alpha-synuclein: mechanistic insights and pathological implication.
Authors: Xie, Y.Y. / Zhou, C.J. / Zhou, Z.R. / Hong, J. / Che, M.X. / Fu, Q.S. / Song, A.X. / Lin, D.H. / Hu, H.Y.
History
DepositionFeb 2, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synphilin-1


Theoretical massNumber of molelcules
Total (without water)5,3711
Polymers5,3711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Synphilin-1 / Alpha-synuclein-interacting protein


Mass: 5371.143 Da / Num. of mol.: 1 / Fragment: Coiled-coil Domain, residues 512-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNCAIP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6H5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNHA
1323D 1H-15N NOESY
1433D HN(CA)CB
1533D CBCA(CO)NH
1633D HBHA(CO)NH
1733D HNCO
1833D (H)CCH-TOCSY
1933D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2mM [U-15N] Synphilin-1, 20mM sodium phosphate, 50mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
21mM [U-100% 15N] Synphilin-1, 20mM sodium phosphate, 50mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
31mM [U-13C; U-15N] Synphilin-1, 20mM sodium phosphate, 50mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMSynphilin-1[U-15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
1 mMSynphilin-1[U-100% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
1 mMSynphilin-1[U-13C; U-15N]3
20 mMsodium phosphate3
50 mMsodium chloride3
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 565 / NOE intraresidue total count: 308 / NOE long range total count: 0 / NOE medium range total count: 107 / NOE sequential total count: 150
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15 / Representative conformer: 1

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