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- PDB-1tk7: NMR structure of WW domains (WW3-4) from Suppressor of Deltex -

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Basic information

Entry
Database: PDB / ID: 1tk7
TitleNMR structure of WW domains (WW3-4) from Suppressor of Deltex
ComponentsCG4244-PB
KeywordsSIGNALING PROTEIN / WW domain / Notch
Function / homology
Function and homology information


pupal development / RHOQ GTPase cycle / imaginal disc-derived leg joint morphogenesis / R8 cell development / imaginal disc-derived wing margin morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / RUNX1 regulates transcription of genes involved in differentiation of HSCs / wing disc dorsal/ventral pattern formation / Downregulation of ERBB4 signaling / RHOU GTPase cycle ...pupal development / RHOQ GTPase cycle / imaginal disc-derived leg joint morphogenesis / R8 cell development / imaginal disc-derived wing margin morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / RUNX1 regulates transcription of genes involved in differentiation of HSCs / wing disc dorsal/ventral pattern formation / Downregulation of ERBB4 signaling / RHOU GTPase cycle / imaginal disc-derived wing vein morphogenesis / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / protein targeting to lysosome / lipid storage / HECT-type E3 ubiquitin transferase / Notch binding / negative regulation of hippo signaling / negative regulation of Notch signaling pathway / positive regulation of endocytosis / negative regulation of smoothened signaling pathway / Notch signaling pathway / receptor internalization / ubiquitin-protein transferase activity / regulation of protein localization / ubiquitin protein ligase activity / cell cortex / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / cytoplasm
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #10 / E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; / 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) ...Ubiquitin Ligase Nedd4; Chain: W; - #10 / E3 ubiquitin-protein ligase, SMURF1 type / Ubiquitin Ligase Nedd4; Chain: W; / 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 / Single Sheet / C2 domain superfamily / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Su(dx)
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsFedoroff, O.Y. / Avis, J.M. / Golovanov, A.P. / Baron, M. / Townson, S.A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The structure and dynamics of tandem WW domains in a negative regulator of notch signaling, Suppressor of deltex
Authors: Fedoroff, O.Y. / Townson, S.A. / Golovanov, A.P. / Baron, M. / Avis, J.M.
History
DepositionJun 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 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: CG4244-PB


Theoretical massNumber of molelcules
Total (without water)10,2801
Polymers10,2801
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 / 20structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein CG4244-PB


Mass: 10280.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su(dx) / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BCl21 / References: UniProt: Q9Y0H4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
131E-COSY
1412D TOCSY
151HSQC in liquid crystal media

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Sample preparation

DetailsContents: 0.5 PBS, 50mM Arg/Glu / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 150 Na/KCl / pH: 7.1 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

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

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Processing

NMR softwareName: ARIA / Version: 1.2 / Developer: Nilges / Classification: refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 20 / Conformers submitted total number: 7

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