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- PDB-1yzb: Solution structure of the Josephin domain of Ataxin-3 -

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Entry
Database: PDB / ID: 1yzb
TitleSolution structure of the Josephin domain of Ataxin-3
ComponentsMachado-Joseph disease protein 1
KeywordsTRANSCRIPTION / papain-like fold
Function / homology
Function and homology information


protein localization to cytosolic proteasome complex / regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton organization / nuclear inclusion body / protein K48-linked deubiquitination / positive regulation of ubiquitin-dependent protein catabolic process / protein K63-linked deubiquitination / cellular response to misfolded protein ...protein localization to cytosolic proteasome complex / regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton organization / nuclear inclusion body / protein K48-linked deubiquitination / positive regulation of ubiquitin-dependent protein catabolic process / protein K63-linked deubiquitination / cellular response to misfolded protein / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / protein quality control for misfolded or incompletely synthesized proteins / protein deubiquitination / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of TORC1 signaling / cellular response to amino acid starvation / Josephin domain DUBs / nucleotide-excision repair / mitochondrial membrane / microtubule cytoskeleton organization / nuclear matrix / nervous system development / cellular response to heat / ATPase binding / actin cytoskeleton organization / ubiquitin-dependent protein catabolic process / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mitochondrial matrix / lysosomal membrane / ubiquitin protein ligase binding / synapse / nucleolus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cathepsin B; Chain A - #40 / Machado-Joseph disease protein / Unstructured region C-term to UIM in Ataxin3 / Josephin domain / Josephin / Josephin domain profile. / Josephin / Ubiquitin interaction motif / S15/NS1, RNA-binding / Ubiquitin-interacting motif. ...Cathepsin B; Chain A - #40 / Machado-Joseph disease protein / Unstructured region C-term to UIM in Ataxin3 / Josephin domain / Josephin / Josephin domain profile. / Josephin / Ubiquitin interaction motif / S15/NS1, RNA-binding / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Cathepsin B; Chain A / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsNicastro, G. / Masino, L. / Menon, R.P. / Knowles, P.P. / McDonald, N.Q. / Pastore, A.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: The solution structure of the Josephin domain of ataxin-3: Structural determinants for molecular recognition
Authors: Nicastro, G. / Menon, R.P. / Masino, L. / Knowles, P.P. / McDonald, N.Q. / Pastore, A.
#1: Journal: J.Biomol.Nmr / Year: 2004
Title: Assignment of the 1H, 13C, and 15N resonances of the Josephin domain of human ataxin-3
Authors: Nicastro, G. / Masino, L. / Frenkiel, T.A. / Kelly, G. / McCormick, J. / Menon, R.P. / Pastore, A.
#2: Journal: J.Mol.Biol. / Year: 2004
Title: Characterization of the structure and the amyloidogenic properties of the Josephin domain of the polyglutamine-containing protein ataxin-3
Authors: Masino, L. / Nicastro, G. / Menon, R.P. / Dal Piaz, F. / Calder, L. / Pastore, A.
#3: Journal: Febs Lett. / Year: 2003
Title: Domain architecture of the polyglutamine protein ataxin-3: a globular domain followed by a flexible tail
Authors: Masino, L. / Musi, V. / Menon, R.P. / Fusi, P. / Kelly, G. / Frenkiel, T.A. / Trottier, Y. / Pastore, A.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 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: Machado-Joseph disease protein 1


Theoretical massNumber of molelcules
Total (without water)21,0541
Polymers21,0541
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)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Machado-Joseph disease protein 1 / Ataxin-3 / Spinocerebellar ataxia type 3 protein


Mass: 21053.768 Da / Num. of mol.: 1 / Fragment: N-terminal domain of Ataxin-3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P54252

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 0.4mM of Josephin 15N, 13C; 20mM sodium phosphate buffer (pH 6.5); 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM sodium phosphate / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2000Delaglio F.processing
ARIA1.2Nilges M.structure solution
ARIA1.2Nilges M.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 5532 unambiguous and 927 ambiguous restraints, 114 dihedral angle restraints, 44 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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