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- PDB-7y4n: Insight into the C-terminal SH3 domain mediated binding of Drosop... -

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Basic information

Entry
Database: PDB / ID: 7y4n
TitleInsight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos
ComponentsGrowth factor receptor-bound protein 2GRB2
KeywordsPEPTIDE BINDING PROTEIN / NMR spectroscopy / SH3 / Drosophila / Adapter protein
Function / homology
Function and homology information


sevenless binding / PI3K Cascade / Downstream signal transduction / Generation of second messenger molecules / : / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / RET signaling ...sevenless binding / PI3K Cascade / Downstream signal transduction / Generation of second messenger molecules / : / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / RET signaling / Erythropoietin activates RAS / FLT3 Signaling / SOS-mediated signalling / Signaling by SCF-KIT / Regulation of KIT signaling / Signalling to RAS / : / DAP12 signaling / SHC-related events triggered by IGF1R / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated Ca+2 mobilization / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / Signal attenuation / Insulin receptor signalling cascade / FCERI mediated MAPK activation / PIP3 activates AKT signaling / GAB1 signalosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / RAF/MAP kinase cascade / torso signaling pathway / tracheal outgrowth, open tracheal system / R7 cell fate commitment / Spry regulation of FGF signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of signaling by CBL / sevenless signaling pathway / RHOU GTPase cycle / EGFR downregulation / Cargo recognition for clathrin-mediated endocytosis / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / epithelial cell migration, open tracheal system / follicle cell of egg chamber development / Clathrin-mediated endocytosis / imaginal disc-derived wing morphogenesis / olfactory learning / short-term memory / COP9 signalosome / epidermal growth factor receptor binding / regulation of MAPK cascade / associative learning / positive regulation of cell size / fibroblast growth factor receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / positive regulation of TORC1 signaling / phosphotyrosine residue binding / sensory perception of sound / epidermal growth factor receptor signaling pathway / positive regulation of receptor-mediated endocytosis / signaling receptor complex adaptor activity / presynapse / insulin receptor signaling pathway / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / signal transduction / protein-containing complex / nucleoplasm / plasma membrane / cytoplasm
Similarity search - Function
Grb2-like / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
Growth factor receptor-bound protein 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / molecular dynamics
AuthorsPooppadi, M.S. / Ikeya, T. / Sugasawa, H. / Watanabe, R. / Mishima, M. / Inomata, K. / Ito, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST; JPMJCR13M3 Japan
Other governmentTokyo Human Resources Fund for City Diplomacy
Japan Society for the Promotion of Science (JSPS)JP26102538,JP19H05773 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Insight into the C-terminal SH3 domain mediated binding of Drosophila Drk to Sos and Dos.
Authors: Sayeesh, P.M. / Ikeya, T. / Sugasawa, H. / Watanabe, R. / Mishima, M. / Inomata, K. / Ito, Y.
History
DepositionJun 15, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth factor receptor-bound protein 2


Theoretical massNumber of molelcules
Total (without water)6,9141
Polymers6,9141
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, distance restraints derived from NOESYs dihedral angle restraints derived from chemical shifts hydrogen bond restraints supported by 3j-HNCO
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

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Components

#1: Protein Growth factor receptor-bound protein 2 / GRB2 / Downstream of receptor kinase / Protein enhancer of sevenless 2B


Mass: 6913.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: drk / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08012

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic113C-separated NOESY
171isotropic115N-sperated NOESY
2122isotropic12D 1H-15N HSQC
1141isotropic13D HNCO
1151isotropic13D HN(CA)CO
1161isotropic13D HNCA
1171isotropic13D HN(CO)CA
1131isotropic13D CBCA(CO)NH
1181isotropic13D CBCANH
1191isotropic13D CC(CO)NH
1201isotropic13D H(CCO)NH
1211isotropic13D 1H-15N TOCSY
1221isotropic13D 1H-15N COSY
1231isotropic13D TROSY HNCO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-100% 13C; U-100% 15N] the C-terminal SH3 domain of Drosophila, 90% H2O/10% D2O13C15N_Sample90% H2O/10% D2O
solution21 mM [U-100% 15N] the C-terminal SH3 domain of Drosophila, 90% H2O/10% D2O15N_Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMthe C-terminal SH3 domain of Drosophila[U-100% 13C; U-100% 15N]1
1 mMthe C-terminal SH3 domain of Drosophila[U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mM13C15N_Sample7.4 AMBIENT atm298 K
2100 mM15N_Sample7.4 AMBIENT atm298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Azara2.8Boucher, W.processing
CcpNmr Analysis2.5.1CCPNchemical shift assignment
CYANA3.98Guntert, P., Mumenthaler, C., and Wuthrich, K.structure calculation
TopSpin3.5 PL7Bruker Biospincollection
OPALpLuginbuhl, R., Guntert, P., Billeter, M., and Wuthrich, K.refinement
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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