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- PDB-8z0n: Structure and dynamics of Drk-SH2 domain and its site-specific in... -

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Basic information

Entry
Database: PDB / ID: 8z0n
TitleStructure and dynamics of Drk-SH2 domain and its site-specific interaction with Sev
ComponentsGrowth factor receptor-bound protein 2
KeywordsPEPTIDE BINDING PROTEIN / Src homology 2 / Drosophila / Downstream receptor kinase / Sev / Growth factor receptor-bound protein 2 / solution structure / dynamics
Function / homology
Function and homology information


PI3K Cascade / Generation of second messenger molecules / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SOS-mediated signalling / Signaling by SCF-KIT ...PI3K Cascade / Generation of second messenger molecules / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SOS-mediated signalling / Signaling by SCF-KIT / Regulation of KIT signaling / Signalling to RAS / Downstream signal transduction / 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 / RET signaling / FLT3 Signaling / FCERI mediated MAPK activation / PIP3 activates AKT signaling / GAB1 signalosome / PI3K events in ERBB2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / sevenless binding / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / torso signaling pathway / NCAM signaling for neurite out-growth / tracheal outgrowth, open tracheal system / 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 / RAF/MAP kinase cascade / EGFR downregulation / RHOU GTPase cycle / Cargo recognition for clathrin-mediated endocytosis / RHO GTPases Activate WASPs and WAVEs / epithelial cell migration, open tracheal system / Regulation of actin dynamics for phagocytic cup formation / R7 cell fate commitment / sevenless signaling pathway / follicle cell of egg chamber development / Clathrin-mediated endocytosis / imaginal disc-derived wing morphogenesis / short-term memory / olfactory learning / COP9 signalosome / epidermal growth factor receptor binding / associative learning / regulation of MAPK cascade / fibroblast growth factor receptor signaling pathway / positive regulation of cell size / vascular endothelial growth factor receptor signaling pathway / phosphotyrosine residue binding / positive regulation of TORC1 signaling / sensory perception of sound / positive regulation of receptor-mediated endocytosis / epidermal growth factor receptor signaling pathway / insulin receptor signaling pathway / signaling receptor complex adaptor activity / presynapse / 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 / SH2 domain superfamily / Src homology 3 domains / 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
AuthorsSayeesh, P.M. / Mayumi, I. / Inomata, K. / IKeya, T. / Ito, Y.
Funding support Japan, 9items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST:JPMJCR13M3 Japan
Japan Science and TechnologyCREST;JPMJCR21E5 Japan
Japan Science and TechnologyJP15K06979 Japan
Japan Science and TechnologyJP19H05645 Japan
Japan Society for the Promotion of Science (JSPS)JP26102538 Japan
Japan Society for the Promotion of Science (JSPS)JP25120003 Japan
Japan Society for the Promotion of Science (JSPS)JP16H00779 Japan
Japan Society for the Promotion of Science (JSPS)JP21K06114 Japan
Japan Science and TechnologyJP15K0979 Japan
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structure and Dynamics of Drk-SH2 Domain and Its Site-Specific Interaction with Sev Receptor Tyrosine Kinase.
Authors: Sayeesh, P.M. / Iguchi, M. / Inomata, K. / Ikeya, T. / Ito, Y.
History
DepositionApr 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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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)10,7391
Polymers10,7391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
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 / Downstream of receptor kinase / Protein enhancer of sevenless 2B


Mass: 10739.168 Da / Num. of mol.: 1 / Fragment: SH2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: drk, E(sev)2B, Grb2, CG6033 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Codon-Plus RIPL / References: UniProt: Q08012
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic113C-seperated NOESY
121isotropic115N-seperated NOESY
131isotropic12D 1H-15N HSQC
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HNCA
171isotropic13D HN(CO)CA
181isotropic13D CBCA(CO)NH
191isotropic13D CBCANH
1101isotropic13D CC(CO)NH
1111isotropic13D H(CCO)NH
1121isotropic12D 1H-13C HSQC
1131isotropic13D HBHA(CO)NH
1151isotropic13D HN(CO)CA
1141isotropic13D HN(CA)CO
1161isotropic13D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM [U-10% 13C; U-100% 15N] SH2 domain of Drk adaptor protein, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution2300 uM [U-100% 15N] SH2 domain of Drk adaptor protein, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMSH2 domain of Drk adaptor protein[U-10% 13C; U-100% 15N]1
300 uMSH2 domain of Drk adaptor protein[U-100% 15N]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1200 mM13C15N_Sample7.4AMBIENT atm298 K
2200 mM15N_Sample7.4AMBIENT 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
Azara2.8Boucherprocessing
CcpNmr Analysis2.5.1CCPNchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
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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