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Yorodumi- PDB-4j96: Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domain Harbori... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j96 | ||||||
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Title | Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domain Harboring the Pathogenic Gain-of-Function K659M Mutation Identified in Cervical Cancer. | ||||||
Components | Fibroblast growth factor receptor 2 | ||||||
Keywords | TRANSFERASE / Kinase Domain Fold Consisting of N- and C-lobes / Receptor Tyrosine Kinase / ATP Binding | ||||||
Function / homology | Function and homology information 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 / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / 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 / 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 / branching involved in salivary gland morphogenesis / embryonic pattern specification / 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 / ureteric bud development / ventricular cardiac muscle tissue morphogenesis / regulation of osteoblast differentiation / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / organ growth / midbrain development / hair follicle morphogenesis / lung alveolus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / fibroblast growth factor binding / PI-3K cascade:FGFR2 / bone mineralization / 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 / positive regulation of cell cycle / SHC-mediated cascade:FGFR2 / cellular response to retinoic acid / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / Signaling by FGFR2 in disease / epithelial cell differentiation / axonogenesis / regulation of ERK1 and ERK2 cascade / post-embryonic development / positive regulation of epithelial cell proliferation / Negative regulation of FGFR2 signaling / animal organ morphogenesis / lung development / bone development / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2972 Å | ||||||
Authors | Chen, H. / Mohammadi, M. | ||||||
Citation | Journal: Cell Rep / Year: 2013 Title: Cracking the Molecular Origin of Intrinsic Tyrosine Kinase Activity through Analysis of Pathogenic Gain-of-Function Mutations. Authors: Chen, H. / Huang, Z. / Dutta, K. / Blais, S. / Neubert, T.A. / Li, X. / Cowburn, D. / Traaseth, N.J. / Mohammadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j96.cif.gz | 266.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j96.ent.gz | 213 KB | Display | PDB format |
PDBx/mmJSON format | 4j96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/4j96 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j96 | HTTPS FTP |
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-Related structure data
Related structure data | 4j95C 4j97C 4j98C 4j99C 2pvyS 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37112.598 Da / Num. of mol.: 2 Fragment: Human FGF Receptor 2 Kinase Domain (UNP Residues 458-768) Mutation: C491A, K659M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BEK, FGFR2, KGFR, KSAM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys-S References: UniProt: P21802, receptor protein-tyrosine kinase |
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-Non-polymers , 5 types, 190 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACP / | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES pH7.5, 25% PEG 4000, 200mM (NH4)2SO4, 100mM HOC(COONa)(CH2COONa)2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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: Dec 8, 2011 |
Radiation | Monochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→50 Å / Num. all: 39689 / Num. obs: 39610 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 25.9 % / Rsym value: 0.114 / Net I/σ(I): 43.6 |
Reflection shell | Resolution: 2.297→2.34 Å / Redundancy: 21.4 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.498 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PVY Resolution: 2.2972→47.549 Å / SU ML: 0.24 / σ(F): 1.33 / Phase error: 21.5 / 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: 2.2972→47.549 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: 40.5622 Å / Origin y: 16.6883 Å / Origin z: 20.9226 Å
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Refinement TLS group | Selection details: all |