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Yorodumi- PDB-2gbq: SOLUTION NMR STRUCTURE OF THE GRB2 N-TERMINAL SH3 DOMAIN COMPLEXE... -
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-Basic information
Entry | Database: PDB / ID: 2gbq | ||||||
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Title | SOLUTION NMR STRUCTURE OF THE GRB2 N-TERMINAL SH3 DOMAIN COMPLEXED WITH A TEN-RESIDUE PEPTIDE DERIVED FROM SOS DIRECT REFINEMENT AGAINST NOES, J-COUPLINGS, AND 1H AND 13C CHEMICAL SHIFTS, 15 STRUCTURES | ||||||
Components |
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Keywords | COMPLEX (SIGNAL TRANSDUCTION/PEPTIDE) / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) / SH3 DOMAIN / COMPLEX (SIGNAL TRANSDUCTION-PEPTIDE) complex | ||||||
Function / homology | Function and homology information Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / MET activates PI3K/AKT signaling ...Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC1 events in ERBB4 signaling / GRB2 events in ERBB2 signaling / EGFR Transactivation by Gastrin / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / SHC-mediated cascade:FGFR2 / MET activates PI3K/AKT signaling / Signaling by LTK / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / SHC-related events triggered by IGF1R / Signal regulatory protein family interactions / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / SOS-mediated signalling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates RAS signaling / MET activates PTPN11 / Costimulation by the CD28 family / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / PI3K events in ERBB2 signaling / Tie2 Signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Interleukin-15 signaling / FLT3 Signaling / CD28 dependent Vav1 pathway / MET activates RAP1 and RAC1 / RHOU GTPase cycle / Signaling by CSF3 (G-CSF) / MET receptor recycling / NCAM signaling for neurite out-growth / Erythropoietin activates RAS / Regulation of KIT signaling / GAB1 signalosome / PI3K Cascade / Role of LAT2/NTAL/LAB on calcium mobilization / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Downstream signal transduction / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Spry regulation of FGF signaling / Insulin receptor signalling cascade / Negative regulation of MET activity / FCERI mediated MAPK activation / anatomical structure formation involved in morphogenesis / Signal attenuation / RHO GTPases Activate WASPs and WAVEs / lymphocyte homeostasis / NRAGE signals death through JNK / Signaling by SCF-KIT / EGFR downregulation / RAC1 GTPase cycle / guanyl-nucleotide exchange factor adaptor activity / GRB2:SOS provides linkage to MAPK signaling for Integrins / FCERI mediated Ca+2 mobilization / Grb2-EGFR complex / RAF/MAP kinase cascade / Interleukin receptor SHC signaling / G alpha (12/13) signalling events / midbrain morphogenesis / PIP3 activates AKT signaling / regulation of pro-B cell differentiation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of signaling by CBL / Regulation of actin dynamics for phagocytic cup formation / vitellogenesis / pericardium morphogenesis / Cargo recognition for clathrin-mediated endocytosis / cardiac atrium morphogenesis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / branching involved in labyrinthine layer morphogenesis / Clathrin-mediated endocytosis / RET signaling / eyelid development in camera-type eye / heart trabecula morphogenesis / COP9 signalosome / neurotrophin TRKA receptor binding / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / positive regulation of Ras protein signal transduction / vesicle membrane / blood vessel morphogenesis / hair follicle development / DAP12 signaling / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / small GTPase-mediated signal transduction / positive regulation of actin filament polymerization / regulation of T cell proliferation / roof of mouth development / ERBB2-ERBB3 signaling pathway Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / DG, SA | ||||||
Authors | Wittekind, M. / Mapelli, C. / Lee, V. / Goldfarb, V. / Friedrichs, M.S. / Meyers, C.A. / Mueller, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: Solution structure of the Grb2 N-terminal SH3 domain complexed with a ten-residue peptide derived from SOS: direct refinement against NOEs, J-couplings and 1H and 13C chemical shifts. Authors: Wittekind, M. / Mapelli, C. / Lee, V. / Goldfarb, V. / Friedrichs, M.S. / Meyers, C.A. / Mueller, L. #1: Journal: Biochemistry / Year: 1994 Title: Orientation of Peptide Fragments from SOS Proteins Bound to the N-Terminal SH3 Domain of Grb2 Determined by NMR Spectroscopy Authors: Wittekind, M. / Mapelli, C. / Farmer II, B.T. / Suen, K.L. / Goldfarb, V. / Tsao, J. / Lavoie, T. / Barbacid, M. / Meyers, C.A. / Mueller, L. #2: Journal: Mol.Cell.Biol. / Year: 1993 Title: Molecular Cloning of the Mouse Grb2 Gene: Differential Interaction of the Grb2 Adaptor Protein with Epidermal Growth Factor and Nerve Growth Factor Receptors Authors: Suen, K.L. / Bustelo, X.R. / Pawson, T. / Barbacid, M. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992 Title: Identification of Murine Homologues of the Drosophila Son of Sevenless Gene: Potential Activators of Ras Authors: Bowtell, D. / Fu, P. / Simon, M. / Senior, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gbq.cif.gz | 324.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gbq.ent.gz | 279.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gbq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gbq_validation.pdf.gz | 364.4 KB | Display | wwPDB validaton report |
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Full document | 2gbq_full_validation.pdf.gz | 518.7 KB | Display | |
Data in XML | 2gbq_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 2gbq_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/2gbq ftp://data.pdbj.org/pub/pdb/validation_reports/gb/2gbq | HTTPS FTP |
-Related 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: 8454.495 Da / Num. of mol.: 1 / Fragment: N-TERMINAL SH3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: BL21 / Cellular location: CYTOPLASMIC / Gene: POTENTIAL / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q60631 |
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#2: Protein/peptide | Mass: 1197.478 Da / Num. of mol.: 1 / Fragment: RESIDUES 1135 - 1144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: CYTOPLASM / References: UniProt: Q62245 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: SEE JOURNAL ARTICLE |
-Sample preparation
Sample conditions | pH: 6 / Temperature: 298. K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 600 MHz |
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-Processing
Software |
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NMR software |
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Refinement | Method: DG, SA / Software ordinal: 1 Details: TWO ENSEMBLES WERE CALCULATED. BOTH USED THE SAME SET OF NOE/ANGLE/J-COUPLING RESTRAINTS, BUT THEY DIFFER IN THAT THE 2ND ENSEMBLE ALSO INCLUDED 1H AND 13C CHEMICAL SHIFTS AS RESTRAINTS (SEE ...Details: TWO ENSEMBLES WERE CALCULATED. BOTH USED THE SAME SET OF NOE/ANGLE/J-COUPLING RESTRAINTS, BUT THEY DIFFER IN THAT THE 2ND ENSEMBLE ALSO INCLUDED 1H AND 13C CHEMICAL SHIFTS AS RESTRAINTS (SEE PRIMARY REFERENCE FOR DETAILS). RMSD BOND DISTANCES 0.009 +/- 0.0002 ANGSTROMS RMSD BOND ANGLE 2.70 +/- 0.08 DEGREES BACKBONE RMSD (N, CA, C, O) = 0.38 +/- 0.11 (SH3 DOMAIN RESIDUES 1 - 26, 36 - 54 AND SOS-E PEPTIDE RESIDUES 2 - 7) | |||||||||
NMR ensemble | Conformers calculated total number: 200 / Conformers submitted total number: 15 |