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Yorodumi- PDB-2jri: Solution structure of the Josephin domain of Ataxin-3 in complex ... -
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-Basic information
Entry | Database: PDB / ID: 2jri | ||||||
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Title | Solution structure of the Josephin domain of Ataxin-3 in complex with ubiquitin molecule. | ||||||
Components |
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Keywords | HYDROLASE/SIGNALING PROTEIN / di-ubiquitin / Lys48-linked / Josephin domain of ataxin-3 / spinocerebellar ataxia type 3 protein / Alternative splicing / Hydrolase / Neurodegeneration / Nucleus / Phosphorylation / Polymorphism / Transcription / Transcription regulation / Triplet repeat expansion / HYDROLASE-SIGNALING PROTEIN COMPLEX | ||||||
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 / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of TORC1 signaling / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / APC-Cdc20 mediated degradation of Nek2A / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / PINK1-PRKN Mediated Mitophagy / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / Regulation of PTEN localization / NRIF signals cell death from the nucleus / cellular response to amino acid starvation / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / EGFR downregulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / nucleotide-excision repair / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | trascription/protein binding, machado-joseph disease protein, ubiquitin-proteasome pathway | ||||||
Authors | Nicastro, G. / Masino, L. / Esposito, V. / Menon, R. / Pastore, A. | ||||||
Citation | Journal: To be Published Title: Understanding the plasticity of the ubiquitin-protein recognition code: the josephin domain of ataxin-3 is a diubiquitin binding motif Authors: Nicastro, G. / Menon, R. / Masino, L. / Pastore, A. #1: 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. / Masino, L. / Esposito, V. / Menon, R. / Pastore, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jri.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2jri.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 2jri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jri_validation.pdf.gz | 362.5 KB | Display | wwPDB validaton report |
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Full document | 2jri_full_validation.pdf.gz | 717.7 KB | Display | |
Data in XML | 2jri_validation.xml.gz | 119.6 KB | Display | |
Data in CIF | 2jri_validation.cif.gz | 159.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/2jri ftp://data.pdbj.org/pub/pdb/validation_reports/jr/2jri | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 21053.768 Da / Num. of mol.: 1 Fragment: N-terminal domain of ataxin-3 sequence database residues 1-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATXN3, ATX3, MJD, MJD1, SCA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 References: UniProt: P54252, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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#2: Protein | Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: sequence database residues 318-469 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q96H31, UniProt: P0CG48*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: trascription/protein binding, machado-joseph disease protein, ubiquitin-proteasome pathway | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.1 - 0.3 mM [U-15N] protein, 0.1 -0.3 mM [U-13C; U-15N] protein, 0.1-0.3 mM protein, 0.1-0.3 mM [U-13C; U-15N; U-2H] protein, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.01 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 / Details: refinement in explicit solvent | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |