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- PDB-2jo9: Mouse Itch 3rd WW domain complex with the Epstein-Barr virus late... -

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Basic information

Entry
Database: PDB / ID: 2jo9
TitleMouse Itch 3rd WW domain complex with the Epstein-Barr virus latent membrane protein 2A derived peptide EEPPPPYED
Components
  • Itchy E3 ubiquitin protein ligase
  • Latent membrane protein 2
KeywordsLIGASE / Itch / WW / complex / Epstein-Barr virus / LMP2A
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 / host cell endomembrane system / Regulation of necroptotic cell death / viral latency / negative regulation of defense response to virus / Degradation of GLI1 by the proteasome / protein K29-linked ubiquitination ...regulation of protein deubiquitination / Downregulation of ERBB4 signaling / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / host cell endomembrane system / Regulation of necroptotic cell death / viral latency / 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 / ligase activity / protein K63-linked ubiquitination / 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 / symbiont-mediated perturbation of host ubiquitin-like protein modification / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / host cell perinuclear region of cytoplasm / protein ubiquitination / innate immune response / apoptotic process / negative regulation of apoptotic process / host cell plasma membrane / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Gammaherpesvirus latent membrane protein 2 / Gammaherpesvirus latent membrane protein (LMP2) protein / 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) ...Gammaherpesvirus latent membrane protein 2 / Gammaherpesvirus latent membrane protein (LMP2) protein / 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
Latent membrane protein 2 / E3 ubiquitin-protein ligase Itchy
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
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 1, 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_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 1.4Dec 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
B: Latent membrane protein 2


Theoretical massNumber of molelcules
Total (without water)5,3492
Polymers5,3492
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/peptide Itchy E3 ubiquitin protein ligase


Mass: 4276.708 Da / Num. of mol.: 1 / Fragment: WW 3 DOMAIN, SEQUENCE DATABASE RESIDUES 399-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itch / 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)
#2: Protein/peptide Latent membrane protein 2 / Terminal protein


Mass: 1072.078 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 54-62 / Source method: obtained synthetically
Details: The peptide was chemically syntheized. The sequence of the peptide is naturally found in Epstein-Barr virus.
References: UniProt: P13285

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D CBCA(CO)NH
1223D CBCANH
1312D 1H-15N HSQC
1413D 1H-15N NOESY
1513D 1H-15N TOCSY
1623D 1H-13C NOESY
1723D 1H-13C TOCSY
1832D 1H-1H NOESY
1932D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 15N] WW3, 3.0 mM Ligand, 20 mM Sodium Phosphate, 100 mM NaCl, 0.02% v/v Sodium Azide, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-100% 13C; U-100% 15N] WW3, 3.0 mM Ligand, 20 mM Sodium Phosphate, 100 mM NaCl, 0.02% v/v Sodium Azide, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM WW3, 3.0 mM Ligand, 20 mM Sodium Phosphate, 100 mM NaCl, 0.02% v/v Sodium Azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMWW3[U-100% 15N]1
3.0 mMLigand1
20 mMSodium Phosphate1
100 mMNaCl1
0.02 v/vSodium Azide1
1.0 mMWW3[U-100% 13C; U-100% 15N]2
3.0 mMLigand2
20 mMSodium Phosphate2
100 mMNaCl2
0.02 v/vSodium Azide2
1.0 mMWW33
3.0 mMLigand3
20 mMSodium Phosphate3
100 mMNaCl3
0.02 v/vSodium Azide3
Sample conditionsIonic strength: 0.4 / pH: 6.2 / Pressure: ambient / Temperature: 285 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002

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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: simulated annealing / Software ordinal: 1 / Details: Aria 1.2 software used, all NOEs manually assigned
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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