+Open data
-Basic information
Entry | Database: PDB / ID: 1yiu | ||||||
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Title | Itch E3 ubiquitin ligase WW3 domain | ||||||
Components | Itchy E3 ubiquitin protein ligase | ||||||
Keywords | LIGASE / WW domain | ||||||
Function / homology | Function and homology information regulation of protein deubiquitination / Downregulation of ERBB4 signaling / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of necroptotic cell death / negative regulation of defense response to virus / Degradation of GLI1 by the proteasome / protein K29-linked ubiquitination / Hedgehog 'on' state / T cell anergy ...regulation of protein deubiquitination / Downregulation of ERBB4 signaling / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of necroptotic cell death / negative regulation of defense response to virus / Degradation of GLI1 by the proteasome / protein K29-linked ubiquitination / Hedgehog 'on' state / T cell anergy / positive regulation of T cell anergy / RUNX1 regulates transcription of genes involved in differentiation of HSCs / CXCR chemokine receptor binding / CD4-positive, alpha-beta T cell proliferation / NOD1/2 Signaling Pathway / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / HECT-type E3 ubiquitin transferase / arrestin family protein binding / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / protein monoubiquitination / protein K63-linked ubiquitination / ligase activity / protein autoubiquitination / protein K48-linked ubiquitination / ribonucleoprotein complex binding / ubiquitin ligase complex / protein catabolic process / receptor internalization / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / cell cortex / early endosome membrane / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / intracellular membrane-bounded organelle / innate immune response / apoptotic process / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Shaw, A.Z. / Martin-Malpartida, P. / Morales, B. / Yraola, F. / Royo, M. / Macias, M.J. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Phosphorylation of either Ser16 or Thr30 does not disrupt the structure of the Itch E3 ubiquitin ligase third WW domain Authors: Shaw, A.Z. / Martin-Malpartida, P. / Morales, B. / Yraola, F. / Royo, M. / Macias, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yiu.cif.gz | 99.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yiu.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yiu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/1yiu ftp://data.pdbj.org/pub/pdb/validation_reports/yi/1yiu | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 4276.708 Da / Num. of mol.: 1 / Fragment: WW3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itch E3 WW3 domain / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q8C863, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: Na2HPO4 20mM NaCl 100mM / pH: 6.0 / Pressure: 1 atm / Temperature: 285 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: The employed refinement engine was CNS 1.1 , but using the water refinement CNS scripts supplied with ARIA 2.0a | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 8 |