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- PDB-5ugl: Crystal Structure of FGF Receptor 2 Tyrosine Kinase Domain Harbor... -
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Basic information
Entry | Database: PDB / ID: 5ugl | ||||||
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Title | Crystal Structure of FGF Receptor 2 Tyrosine Kinase Domain Harboring the D650V Activating Mutation | ||||||
![]() | Fibroblast growth factor receptor 2 | ||||||
![]() | TRANSFERASE / Tyrosine Kinase domain / ATP analoge / Gain-of-function Mutation | ||||||
Function / homology | ![]() 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 ...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 / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / 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 / 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 / embryonic pattern specification / branching involved in salivary gland morphogenesis / outflow tract septum morphogenesis / positive regulation of phospholipase activity / lung-associated mesenchyme development / mesodermal cell differentiation / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / digestive tract development / bone morphogenesis / skeletal system morphogenesis / odontogenesis / positive regulation of mesenchymal cell proliferation / ventricular cardiac muscle tissue morphogenesis / ureteric bud development / regulation of osteoblast differentiation / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / midbrain development / organ growth / hair follicle morphogenesis / lung alveolus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / bone mineralization / fibroblast growth factor binding / prostate epithelial cord elongation / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / PI3K Cascade / negative regulation of keratinocyte proliferation / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / cell fate commitment / embryonic organ development / SHC-mediated cascade:FGFR2 / positive regulation of cell cycle / cellular response to retinoic acid / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / cellular response to transforming growth factor beta stimulus / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / epithelial cell differentiation / regulation of ERK1 and ERK2 cascade / axonogenesis / post-embryonic development / positive regulation of epithelial cell proliferation / animal organ morphogenesis / Negative regulation of FGFR2 signaling / lung development / bone development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mohammadi, M. / Chen, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Elucidation of a four-site allosteric network in fibroblast growth factor receptor tyrosine kinases. Authors: Chen, H. / Marsiglia, W.M. / Cho, M.K. / Huang, Z. / Deng, J. / Blais, S.P. / Gai, W. / Bhattacharya, S. / Neubert, T.A. / Traaseth, N.J. / Mohammadi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 235.2 KB | Display | ![]() |
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PDB format | ![]() | 188.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5ugxC ![]() 5uhnC ![]() 5ui0C ![]() 2psqS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37094.625 Da / Num. of mol.: 2 / Fragment: UNP residues 341-651 / Mutation: D650V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P21802, receptor protein-tyrosine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25 mM HEPES pH7.5, 15%-25% w/v PEG4000, 0.2-0.3 M NH4SO3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 46452 / % possible obs: 87.9 % / Redundancy: 14 % / Rsym value: 0.048 / Net I/σ(I): 75.5 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 11 % / Mean I/σ(I) obs: 17.3 / Rsym value: 0.182 / % possible all: 57.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PSQ Resolution: 1.861→34.843 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.24 / 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: 1.861→34.843 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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