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- PDB-1yiu: Itch E3 ubiquitin ligase WW3 domain -

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Basic information

Entry
Database: PDB / ID: 1yiu
TitleItch E3 ubiquitin ligase WW3 domain
ComponentsItchy E3 ubiquitin protein ligase
KeywordsLIGASE / WW domain
Function / homology
Function and homology information


regulation of protein deubiquitination / negative regulation of alpha-beta T cell proliferation / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / Degradation of GLI1 by the proteasome / Regulation of necroptotic cell death / negative regulation of defense response to virus / Hedgehog 'on' state / protein K29-linked ubiquitination ...regulation of protein deubiquitination / negative regulation of alpha-beta T cell proliferation / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / Degradation of GLI1 by the proteasome / Regulation of necroptotic cell death / negative regulation of defense response to virus / Hedgehog 'on' state / protein K29-linked ubiquitination / CXCL12-activated CXCR4 signaling pathway / RUNX1 regulates transcription of genes involved in differentiation of HSCs / CXCR chemokine receptor binding / protein branched polyubiquitination / NOD1/2 Signaling Pathway / positive regulation of T cell anergy / HECT-type E3 ubiquitin transferase / arrestin family protein binding / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of JNK cascade / positive regulation of receptor catabolic process / ubiquitin-ubiquitin ligase activity / cytoplasmic pattern recognition receptor signaling pathway / ligase activity / ubiquitin-like protein ligase binding / protein K63-linked ubiquitination / protein monoubiquitination / ubiquitin ligase complex / ribonucleoprotein complex binding / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of canonical NF-kappaB signal transduction / receptor internalization / protein polyubiquitination / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / response to oxidative stress / cytoplasmic vesicle / early endosome membrane / cell cortex / defense response to virus / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / innate immune response / apoptotic process / negative regulation of apoptotic process / protein-containing complex / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain ...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 / Protein kinase C conserved region 2 (CalB) / C2 domain / WW domain / C2 domain / C2 domain profile. / WW/rsp5/WWP domain signature. / 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
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsShaw, A.Z. / Martin-Malpartida, P. / Morales, B. / Yraola, F. / Royo, M. / Macias, M.J.
CitationJournal: 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
DepositionJan 13, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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_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_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)4,2771
Polymers4,2771
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)8 / 50structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Itchy E3 ubiquitin protein ligase


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated NOESY
1433D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1Unlabeled sampleSodium Phosphate 20mM, Sodium Chloride 100mM
2Uniform labeling with 15NSodium Phosphate 20mM, Sodium Chloride 100mM
3Uniform labeling with 15N, 13CSodium Phosphate 20mM, Sodium Chloride 100mM
Sample conditionsIonic strength: Na2HPO4 20mM NaCl 100mM / pH: 6 / Pressure: 1 atm / Temperature: 285 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Bruker GMBHcollection
NMRPipe2.2Delaglio, F.processing
XEASY1.3Bartels, C.data analysis
CNS1.1Bruengerstructure solution
ARIA2.0aNilges, M.structure solution
ARIA2.0aNilges, M.refinement
CNS1.1Bruengerrefinement
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 8

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