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Yorodumi- PDB-5eg3: Crystal Structure of the Activated FGF Receptor 2 (FGFR2) Kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eg3 | ||||||
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Title | Crystal Structure of the Activated FGF Receptor 2 (FGFR2) Kinase Domain in complex with the cSH2 domain of Phospholipase C gamma (PLCgamma) | ||||||
Components |
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Keywords | Transferase/Hydrolase / Signaling Complex / Tyrosine Kinase domain / SH2 domain / Recruitment / Phosphorylation / Transferase-Hydrolase 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 FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / phosphoinositide phospholipase C / FCERI mediated MAPK activation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / embryonic organ morphogenesis / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / pyramidal neuron development / response to gravity / positive regulation of epithelial cell proliferation involved in lung morphogenesis / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / phosphatidylinositol metabolic process / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / phosphatidylinositol phospholipase C activity / embryonic pattern specification / outflow tract septum morphogenesis / COP9 signalosome / phospholipase C activity / positive regulation of phospholipase activity / neurotrophin TRKA receptor binding / lung-associated mesenchyme development / mesodermal cell differentiation / digestive tract development / positive regulation of endothelial cell apoptotic process / embryonic cranial skeleton morphogenesis / regulation of smoothened signaling pathway / phosphatidylinositol-mediated signaling / bone morphogenesis / skeletal system morphogenesis / odontogenesis / ureteric bud development / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / clathrin-coated vesicle / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / organ growth / midbrain development / hair follicle morphogenesis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.606 Å | ||||||
Authors | Huang, Z. / Li, X. / Mohammadi, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol.Cell / Year: 2016 Title: Two FGF Receptor Kinase Molecules Act in Concert to Recruit and Transphosphorylate Phospholipase C gamma. Authors: Huang, Z. / Marsiglia, W.M. / Basu Roy, U. / Rahimi, N. / Ilghari, D. / Wang, H. / Chen, H. / Gai, W. / Blais, S. / Neubert, T.A. / Mansukhani, A. / Traaseth, N.J. / Li, X. / Mohammadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eg3.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eg3.ent.gz | 144.2 KB | Display | PDB format |
PDBx/mmJSON format | 5eg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/5eg3 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/5eg3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38155.676 Da / Num. of mol.: 1 / Fragment: UNP residues 458-778 Mutation: Y466F, C491A, E565A, Y586L, Y588P, Y656F, Y657F, K659E Source method: isolated from a genetically manipulated source Details: Tyr326 is phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KGFR, KSAM / Production host: Escherichia coli (E. coli) References: UniProt: P21802, receptor protein-tyrosine kinase | ||
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#2: Protein | Mass: 13310.129 Da / Num. of mol.: 1 / Fragment: UNP residues 661-773 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 | ||
#3: Chemical | ChemComp-ACP / | ||
#4: Chemical | #5: 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: 2.59 Å3/Da / Density % sol: 52.46 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25 mM HEPES (pH 7.5), PEG20000 (12% 18%) and 2% (w/v) Benzamidine hydrochloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→37.859 Å / Num. obs: 15981 / % possible obs: 98.2 % / Redundancy: 6.6 % / Rsym value: 0.093 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 5.9 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PVY, 2PLE Resolution: 2.606→37.859 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.606→37.859 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 21.3631 Å / Origin y: 9.0993 Å / Origin z: 28.3348 Å
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Refinement TLS group | Selection details: all |