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- PDB-2jmf: Solution structure of the Su(dx) WW4- Notch PY peptide complex -

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Basic information

Entry
Database: PDB / ID: 2jmf
TitleSolution structure of the Su(dx) WW4- Notch PY peptide complex
Components
  • E3 ubiquitin-protein ligase suppressor of deltex
  • Neurogenic locus Notch protein
KeywordsLigase/Signaling Protein / WW domain / Notch / NMR solution / complex / Ligase-Signaling Protein COMPLEX
Function / homology
Function and homology information


pupal development / response to symbiont / neuroblast fate specification / epithelial cell type specification, open tracheal system / lamellocyte differentiation / regulation of cardioblast cell fate specification / positive regulation of crystal cell differentiation / negative regulation of compound eye photoreceptor development / R1/R6 cell differentiation / formation of a compartment boundary ...pupal development / response to symbiont / neuroblast fate specification / epithelial cell type specification, open tracheal system / lamellocyte differentiation / regulation of cardioblast cell fate specification / positive regulation of crystal cell differentiation / negative regulation of compound eye photoreceptor development / R1/R6 cell differentiation / formation of a compartment boundary / compartment boundary maintenance / Degradation of the extracellular matrix / Keratan sulfate biosynthesis / Keratan sulfate degradation / ECM proteoglycans / RHOQ GTPase cycle / follicle cell of egg chamber migration / muscle cell fate determination / imaginal disc-derived leg joint morphogenesis / Chondroitin sulfate biosynthesis / Dermatan sulfate biosynthesis / CS/DS degradation / eye-antennal disc development / crystal cell differentiation / R8 cell development / R7 cell differentiation / R3/R4 cell differentiation / germ-line stem-cell niche homeostasis / oocyte localization involved in germarium-derived egg chamber formation / hemocyte proliferation / negative regulation of lamellocyte differentiation / compound eye retinal cell programmed cell death / myoblast development / imaginal disc-derived male genitalia morphogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / germarium-derived egg chamber formation / leg disc morphogenesis / epithelial cell proliferation involved in Malpighian tubule morphogenesis / CSL-Notch-Mastermind transcription factor complex / lateral inhibition / Malpighian tubule tip cell differentiation / eye-antennal disc morphogenesis / second mitotic wave involved in compound eye morphogenesis / A tetrasaccharide linker sequence is required for GAG synthesis / imaginal disc-derived wing margin morphogenesis / Activated NOTCH1 Transmits Signal to the Nucleus / imaginal disc-derived leg segmentation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / sensory organ precursor cell fate determination / female germ-line stem cell population maintenance / ommatidial rotation / wing disc dorsal/ventral pattern formation / Downregulation of ERBB4 signaling / RHOU GTPase cycle / defense response to insect / wing disc pattern formation / imaginal disc-derived wing vein morphogenesis / Antigen processing: Ubiquitination & Proteasome degradation / follicle cell of egg chamber stalk formation / Regulation of PTEN stability and activity / imaginal disc-derived leg morphogenesis / chaeta morphogenesis / dorsal closure / compound eye morphogenesis / follicle cell of egg chamber development / larval lymph gland hemopoiesis / neuroblast development / lymph gland development / cell dedifferentiation / neuroblast fate determination / imaginal disc-derived wing vein specification / dorsal appendage formation / border follicle cell migration / intestinal stem cell homeostasis / compound eye development / regulation of stem cell division / chaeta development / foregut morphogenesis / asymmetric cell division / imaginal disc-derived wing morphogenesis / glial cell fate determination / neuron fate specification / regulation of neuroblast proliferation / retinal cell programmed cell death / glial cell migration / sensory organ development / germ-line stem cell population maintenance / dorsal/ventral axis specification / neuron fate determination / glial cell differentiation / WW domain binding / neuronal stem cell population maintenance / regulation of filopodium assembly / protein targeting to lysosome / lipid storage / negative regulation of cell-cell adhesion mediated by cadherin / peripheral nervous system development / HECT-type E3 ubiquitin transferase / nervous system process
Similarity search - Function
: / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP ...: / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / E3 ubiquitin-protein ligase, SMURF1 type / Domain of unknown function DUF3447 / Notch domain / Domain found in Notch and Lin-12 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / EGF-like, conserved site / Human growth factor-like EGF / 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 / Calcium-binding EGF domain / 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 / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Single Sheet / Ankyrin repeat / C2 domain superfamily / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Neurogenic locus Notch protein / Notch / E3 ubiquitin-protein ligase Su(dx)
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsAvis, J.M. / Blankley, R.T. / Jennings, M.D. / Golovanov, A.P.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Specificity and Autoregulation of Notch Binding by Tandem WW Domains in Suppressor of Deltex
Authors: Jennings, M.D. / Blankley, R.T. / Baron, M. / Golovanov, A.P. / Avis, J.M.
History
DepositionNov 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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 1.3Dec 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: E3 ubiquitin-protein ligase suppressor of deltex
B: Neurogenic locus Notch protein


Theoretical massNumber of molelcules
Total (without water)8,0902
Polymers8,0902
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)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase suppressor of deltex


Mass: 5928.586 Da / Num. of mol.: 1 / Fragment: WW4 domain, residues 515-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Su dx / Plasmid details: cloned between EcoRI and XhoI / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q9Y0H4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide Neurogenic locus Notch protein


Mass: 2161.392 Da / Num. of mol.: 1 / Fragment: L/PPxY motif, residues 2318-2332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: N / Plasmid details: cloned between BamHI and XhoI / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07207, UniProt: Q32UW5*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1313D HNCO
1423D HNCO
1513D HNCA
1623D HNCA
1713D HN(CA)CB
1823D HN(CA)CB
1913D HN(CO)CA
11023D HN(CO)CA
11113D (H)CCH-TOCSY
11223D (H)CCH-TOCSY
11313D 1H-15N NOESY
11423D 1H-15N NOESY
11513D 1H-15N TOCSY
11623D 1H-15N TOCSY
11713D 1H-13C NOESY
11823D 1H-13C NOESY
11912D 1H-13C HSQC
12022D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-13C, U-15N] WW4 domain from Su(dx), 2.0 mM Notch, 45 mM sodium chloride, 9 mM DTT, 0.9 mM EDTA, 45 mM Arginine, 45 mM Glutamate, 90 % H2O, 10 % D2O90% H2O/10% D2O
23.0 mM [U-13C, U-15N] Notch, 0.8 mM WW4 domain from Su(dx), 45 mM sodium chloride, 9 mM DTT, 0.9 mM EDTA, 45 mM Arginine, 45 mM Glutamate, 90 % H2O, 10 % D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMSu(dx)[U-13C; U-15N]1
1.5 mMNotch1
45 mMsodium chloride1
9 mMDTT1
0.9 mMEDTA1
45 mMArginine1
45 mMGlutamate1
10 %D2O1
0.4 mMNotch[U-13C; U-15N]2
1.5 mMSu(dx)2
45 mMsodium chloride2
9 mMDTT2
0.9 mMEDTA2
45 mMArginine2
45 mMGlutamate2
10 %D2O2
Sample conditionspH: 6.75 / Pressure: ambient / Temperature: 293 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 software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CARAKeller and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
NMRViewJohnsonstructure solution
AmberCase, Darden, Cheatham, Simmerling, Wang, Dukerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: energy minimisation performed using AMBER
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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