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Yorodumi- PDB-2a37: Solution structure of the T22G mutant of N-terminal SH3 domain of... -
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-Basic information
Entry | Database: PDB / ID: 2a37 | ||||||
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Title | Solution structure of the T22G mutant of N-terminal SH3 domain of DRK (DRKN SH3 DOMAIN) | ||||||
Components | Protein E(sev)2B | ||||||
Keywords | SIGNALING PROTEIN / DROSOPHILA MELANOGASTER / SH3 FRAGMENT / DRK | ||||||
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 | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Bezsonova, I. / Singer, A. / Choy, W.-Y. / Tollinger, M. / Forman-Kay, J.D. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural Comparison of the Unstable drkN SH3 Domain and a Stable Mutant Authors: Bezsonova, I. / Singer, A. / Choy, W.-Y. / Tollinger, M. / Forman-Kay, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a37.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a37.ent.gz | 158.8 KB | Display | PDB format |
PDBx/mmJSON format | 2a37.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/2a37 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/2a37 | HTTPS FTP |
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-Related structure data
Related structure data | 2a36C 2azsC 2azvC 1q37 C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6824.576 Da / Num. of mol.: 1 / Fragment: N-Terminal SH3 domain, residues 1-59 / Mutation: T22G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: drk, E(sev)2B, CG6033 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q08012 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: T22G DRKN SH3 DOMAIN 15N, 13C, 50 MM SODIUM PHOSPHATE BUFFER, 90% H2O, 10% D2O, PH 6.0 |
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Sample conditions | Ionic strength: 0.164 / pH: 6.0 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES ARE BASED ON 215 RESIDUAL DIPOLAR COUPLING RESTRAINTS, 54 CARBONYL CHEMICAL SHIFT ANISOTROPY RESTRAINTS, 44 DIHEDRAL ANGLE RESTRAINTS AND 21 HYDROGEN BOND RESTRAINTS. 777 NOE- ...Details: THE STRUCTURES ARE BASED ON 215 RESIDUAL DIPOLAR COUPLING RESTRAINTS, 54 CARBONYL CHEMICAL SHIFT ANISOTROPY RESTRAINTS, 44 DIHEDRAL ANGLE RESTRAINTS AND 21 HYDROGEN BOND RESTRAINTS. 777 NOE-DERIVED DISTANCE CONSTRAINTS OF THE WILD TYPE DRKN SH3 DOMAIN WERE INCORPORATED INTO THE STRUCTURE CALCULATION OF THE T22G MUTANT. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |