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Yorodumi- PDB-3gqi: Crystal Structure of activated receptor tyrosine kinase in comple... -
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-Basic information
Entry | Database: PDB / ID: 3gqi | ||||||
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Title | Crystal Structure of activated receptor tyrosine kinase in complex with substrates | ||||||
Components |
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Keywords | Transferase/Transferase inhibitor / phosphorylated kinase / pY-recognition / tandem SH2 domains / ATP analog / ATP-binding / Craniosynostosis / Disease mutation / Disulfide bond / Dwarfism / Glycoprotein / Heparin-binding / Hypogonadotropic hypogonadism / Immunoglobulin domain / Kallmann syndrome / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / Hydrolase / Lipid degradation / SH2 domain / SH3 domain / Transducer / Transferase-Transferase Inhibitor COMPLEX | ||||||
Function / homology | Function and homology information PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / FCERI mediated Ca+2 mobilization / ISG15 antiviral mechanism ...PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / FCERI mediated Ca+2 mobilization / ISG15 antiviral mechanism / Generation of second messenger molecules / Phospholipase C-mediated cascade; FGFR2 / Downstream signal transduction / Signaling by ALK / Role of phospholipids in phagocytosis / inositol trisphosphate biosynthetic process / DAP12 signaling / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / RET signaling / inositol trisphosphate metabolic process / response to curcumin / Signaling by FGFR1 amplification mutants / phosphoinositide phospholipase C / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FCERI mediated MAPK activation / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / response to gravity / response to sodium phosphate / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / phosphatidylinositol metabolic process / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / phosphatidylinositol phospholipase C activity / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / COP9 signalosome / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / phospholipase C activity / positive regulation of phospholipase activity / neurotrophin TRKA receptor binding / lung-associated mesenchyme development / cell projection assembly / positive regulation of endothelial cell apoptotic process / cellular response to fibroblast growth factor stimulus / outer ear morphogenesis / middle ear morphogenesis / embryonic limb morphogenesis / skeletal system morphogenesis / clathrin-coated vesicle / positive regulation of endothelial cell chemotaxis / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / positive regulation of vascular endothelial cell proliferation / ureteric bud development / inner ear morphogenesis / midbrain development / positive regulation of epithelial cell migration / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / PI-3K cascade:FGFR1 / regulation of cell differentiation / phosphatidylinositol-mediated signaling / PI3K Cascade / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / glutamate receptor binding / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / : / SHC-mediated cascade:FGFR1 / release of sequestered calcium ion into cytosol / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / cellular response to epidermal growth factor stimulus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Bae, J.H. / Lew, E.D. / Yuzawa, S. / Tome, F. / Lax, I. / Schlessinger, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2009 Title: The selectivity of receptor tyrosine kinase signaling is controlled by a secondary SH2 domain binding site. Authors: Bae, J.H. / Lew, E.D. / Yuzawa, S. / Tome, F. / Lax, I. / Schlessinger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gqi.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gqi.ent.gz | 94.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gqi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/3gqi ftp://data.pdbj.org/pub/pdb/validation_reports/gq/3gqi | HTTPS FTP |
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-Related structure data
Related structure data | 3gqlC 1fgkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 37482.742 Da / Num. of mol.: 1 / Fragment: Protein kinase domain / Mutation: C488A, Y583F, C584S, Y575F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFBR, FGFR1, FLG, FLT2 / Production host: Escherichia coli (E. coli) References: UniProt: P11362, receptor protein-tyrosine kinase |
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#2: Protein | Mass: 26322.682 Da / Num. of mol.: 1 / Fragment: tandem SH2 domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Production host: Escherichia coli (E. coli) References: UniProt: P10686, phosphoinositide phospholipase C |
-Non-polymers , 4 types, 80 molecules
#3: Chemical | ChemComp-DVT / |
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#4: Chemical | ChemComp-ACP / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEg 8000, taurine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 27448 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Χ2: 1.129 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Mean I/σ(I) obs: 31.971 / Num. unique all: 27448 / Χ2: 0.956 / % possible all: 98.3 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Phasing dm shell | Resolution: 2.5→50 Å / Delta phi final: 0.177 / FOM : 0.183 / Reflection: 26120 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FGK Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.764 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 47.058 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.76 Å2 / Biso mean: 80.321 Å2 / Biso min: 28.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Xplor file |
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