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- PDB-2dos: Structural basis for the recognition of Lys48-linked polyubiquiti... -

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Basic information

Entry
Database: PDB / ID: 2dos
TitleStructural basis for the recognition of Lys48-linked polyubiquitin chain by the Josephin domain of ataxin-3, a putative deubiquitinating enzyme
ComponentsAtaxin-3
KeywordsHYDROLASE / Deubiquitinating enzyme
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 / 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 / protein K48-linked deubiquitination / nuclear inclusion body / 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 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of TORC1 signaling / cellular response to amino acid starvation / Josephin domain DUBs / mitochondrial membrane / nucleotide-excision repair / nuclear matrix / microtubule cytoskeleton organization / 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 / cytoplasm / cytosol
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 / distance geometry, simulated annealing
AuthorsSumiyoshi, A.
CitationJournal: Febs Lett. / Year: 2014
Title: Mode of substrate recognition by the Josephin domain of ataxin-3, which has an endo-type deubiquitinase activity.
Authors: Satoh, T. / Sumiyoshi, A. / Yagi-Utsumi, M. / Sakata, E. / Sasakawa, H. / Kurimoto, E. / Yamaguchi, Y. / Li, W. / Joazeiro, C.A. / Hirokawa, T. / Kato, K.
History
DepositionMay 3, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 3, 2014Group: Database references
Revision 1.4Dec 31, 2014Group: Database references
Revision 1.5May 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 / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ataxin-3


Theoretical massNumber of molelcules
Total (without water)20,1631
Polymers20,1631
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 Ataxin-3 / Machado-Joseph disease protein 1 / Spinocerebellar ataxia type 3 protein


Mass: 20162.674 Da / Num. of mol.: 1 / Fragment: Josephin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P54252, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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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
1322D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM Josephin domain U-15N,13C; 10mM Sodium phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
21.2mM Josephin domain U-15N,13C; 10mM Sodium phosphate buffer; 99% D2O99% D2O
Sample conditionsIonic strength: 10mM Sodium phosphate buffer / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
JEOL ECAJEOLECA9201
Bruker AVANCEBrukerAVANCE6002
Bruker DMXBrukerDMX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6collection
NMRPipe2.3Delaglioprocessing
CYANA2.1Guntertstructure solution
Delta4.3.3collection
CYANA2.1Guntertrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
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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