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- PDB-2aga: De-ubiquitinating function of ataxin-3: insights from the solutio... -

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Basic information

Entry
Database: PDB / ID: 2aga
TitleDe-ubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain
ComponentsMachado-Joseph disease protein 1Machado–Joseph disease
KeywordsTRANSCRIPTION / Polyglutamine / ubiquitin / UIM / ataxia / VCP/p97
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 / protein K48-linked deubiquitination / nuclear inclusion body / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to misfolded protein / protein K63-linked deubiquitination ...protein localization to cytosolic proteasome complex / regulation of cell-substrate adhesion / positive regulation of ERAD pathway / monoubiquitinated protein deubiquitination / intermediate filament cytoskeleton organization / protein K48-linked deubiquitination / nuclear inclusion body / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to misfolded protein / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / exploration behavior / K63-linked deubiquitinase activity / protein quality control for misfolded or incompletely synthesized proteins / 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 / cellular response to heat / nervous system development / ATPase binding / ubiquitin-dependent protein catabolic process / actin cytoskeleton organization / chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mitochondrial matrix / lysosomal membrane / synapse / ubiquitin protein ligase binding / nucleolus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cathepsin B; Chain A - #40 / Unstructured region C-term to UIM in Ataxin3 / Machado-Joseph disease protein / Josephin domain / Josephin / Josephin domain profile. / Josephin / Ubiquitin interaction motif / S15/NS1, RNA-binding / Ubiquitin-interacting motif. ...Cathepsin B; Chain A - #40 / Unstructured region C-term to UIM in Ataxin3 / Machado-Joseph disease protein / 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
AuthorsMao, Y. / Senic-Matuglia, F. / Di Fiore, P. / Polo, S. / Hodsdon, M.E. / De Camilli, P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Deubiquitinating function of ataxin-3: insights from the solution structure of the Josephin domain.
Authors: Mao, Y. / Senic-Matuglia, F. / Di Fiore, P.P. / Polo, S. / Hodsdon, M.E. / De Camilli, P.
History
DepositionJul 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)21,8211
Polymers21,8211
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 21820.611 Da / Num. of mol.: 1 / Fragment: Josephin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATXN3, ATX3, MJD, MJD1, SCA3 / Plasmid: pGEX6P-1 / 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 experimentType: 3D 13C-separated NOESY
NMR detailsText: This structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 2mM Josephin domain U-15N,13C; 20mM phosphate buffer pH 6.4; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM KPO4 / pH: 6.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.5Guentertstructure solution
NMRPipe2.3Delagliodata analysis
Sparky3.106Kneller and Goddarddata analysis
CYANA1.0.5Guentertrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 2960 NOE-derived distance constraints, 224 dihedral angle restraints,122 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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