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Yorodumi- PDB-2pvf: Crystal Structure of Tyrosine Phosphorylated Activated FGF Recept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pvf | ||||||
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Title | Crystal Structure of Tyrosine Phosphorylated Activated FGF Receptor 2 (FGFR2) Kinase Domain in Complex with ATP Analog and Substrate Peptide | ||||||
Components | (Fibroblast growth factor receptor 2) x 2 | ||||||
Keywords | TRANSFERASE / Kinase Domain Fold Consisting of N- and C-lobes | ||||||
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 / pyramidal neuron development / 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 / 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 / digestive tract development / embryonic cranial skeleton morphogenesis / regulation of smoothened signaling pathway / bone morphogenesis / skeletal system morphogenesis / odontogenesis / ureteric bud development / positive regulation of mesenchymal cell proliferation / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / organ growth / midbrain development / hair follicle morphogenesis / lung alveolus development / fibroblast growth factor binding / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / 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 / epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / fibroblast growth factor receptor signaling pathway / embryonic organ development / cell fate commitment / positive regulation of cell cycle / SHC-mediated cascade:FGFR2 / cellular response to retinoic acid / FRS-mediated FGFR2 signaling / positive regulation of cardiac muscle cell proliferation / 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 / post-embryonic development / regulation of ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / Negative regulation of FGFR2 signaling / lung development / animal organ morphogenesis / bone development / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of canonical Wnt signaling pathway Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Chen, H. / Mohammadi, M. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: A molecular brake in the kinase hinge region regulates the activity of receptor tyrosine kinases. Authors: Chen, H. / Ma, J. / Li, W. / Eliseenkova, A.V. / Xu, C. / Neubert, T.A. / Miller, W.T. / Mohammadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pvf.cif.gz | 79.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pvf.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pvf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/2pvf ftp://data.pdbj.org/pub/pdb/validation_reports/pv/2pvf | HTTPS FTP |
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-Related structure data
Related structure data | 2psqSC 2pvyC 2pwlC 2py3C 2pz5C 2pzpC 2pzrC 2q0bC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 38537.809 Da / Num. of mol.: 1 / Fragment: human FGF Receptor 2 Kinase Domain / Mutation: C491A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, 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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#2: Protein/peptide | Mass: 1779.852 Da / Num. of mol.: 1 / Fragment: Peptide Stubstrate / Source method: obtained synthetically Details: Custom-designed peptide based on Phosphorylation Site Y769 of human FGFR2 Kinase References: UniProt: P21802 | ||||
#3: Chemical | #4: Chemical | ChemComp-ACP / | #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: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES pH7.5, 27% PEG 4000, 200mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2005 |
Radiation | Monochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 35199 / Num. obs: 35199 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.046 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.1 % / Num. unique all: 3478 / Rsym value: 0.267 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 2PSQ Resolution: 1.8→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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