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- PDB-2joc: Mouse Itch 3rd domain phosphorylated in T30 -

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Basic information

Entry
Database: PDB / ID: 2joc
TitleMouse Itch 3rd domain phosphorylated in T30
ComponentsItchy E3 ubiquitin protein ligase
KeywordsLIGASE / Itch / WW / Phosphothreonine
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
E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...E3 ubiquitin-protein ligase, SMURF1 type / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / C2 domain / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Itchy
Similarity search - Component
MethodSOLUTION NMR / molecular dynamics
AuthorsMacias, M.J. / Shaw, A.Z. / Martin-Malpartida, P. / Morales, B. / Ruiz, L. / Ramirez-Espain, X. / Yraola, F. / Royo, M.
CitationJournal: Structure / Year: 2007
Title: NMR Structural Studies of the ItchWW3 Domain Reveal that Phosphorylation at T30 Inhibits the Interaction with PPxY-Containing Ligands
Authors: Morales, B. / Ramirez-Espain, X. / Shaw, A.Z. / Martin-Malpartida, P. / Yraola, F. / Sanchez-Tillo, E. / Farrera, C. / Celada, A. / Royo, M. / Macias, M.J.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Itchy E3 ubiquitin protein ligase


Theoretical massNumber of molelcules
Total (without water)4,3571
Polymers4,3571
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)7 / 7all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Itchy E3 ubiquitin protein ligase


Mass: 4356.688 Da / Num. of mol.: 1 / Fragment: WW 3 domain, sequence database residues 399-432 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (mouse).
References: UniProt: Q8C863, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
2212D 1H-1H TOCSY
1312D 1H-1H NOESY
2412D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.0 mM PhosphoI3, 20 mM Sodium Phosphate, 100 mM NaCl, 0.02% v/v Sodium Azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.0 mMPhosphoI31
20 mMSodium Phosphate1
100 mMNaCl1
0.02 v/vSodium Azide1
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.4 6.5 ambient 280 K
20.4 6.5 ambient 285 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 7 / Conformers submitted total number: 7

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