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Yorodumi- PDB-1wvz: Solution Structure of the D2 Domain of the Fibroblast Growth Factor -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wvz | ||||||
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Title | Solution Structure of the D2 Domain of the Fibroblast Growth Factor | ||||||
Components | Fibroblast growth factor receptor 2 | ||||||
Keywords | TRANSFERASE / Fibroblast Growth Factor receptor / heparin / tumor / angiogenesis | ||||||
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 | SOLUTION NMR / distance geometry | ||||||
Model type details | minimized average | ||||||
Authors | Hung, K.W. / Kumar, T.K.S. / Yu, C. | ||||||
Citation | Journal: To be Published Title: Solution Structure of the D2 Domain of the Fibroblast Growth Factor Authors: Hung, K.W. / Kumar, T.K.S. / Yu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wvz.cif.gz | 697.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wvz.ent.gz | 614.2 KB | Display | PDB format |
PDBx/mmJSON format | 1wvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/1wvz ftp://data.pdbj.org/pub/pdb/validation_reports/wv/1wvz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12054.738 Da / Num. of mol.: 1 / Fragment: D2 domain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: Q9UQH9, UniProt: P21802*PLUS, EC: 2.7.1.112 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1mM Fibroblast Growth Factor Receptor, U-15N, 13C; 20mM phosphate buffer (pH 6.5) containing 20mM NaCl, 50mM ammonium sulfate; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 20mM phosphate buffer containing 20mM NaCl and 50mM ammonium sulfate pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry / Software ordinal: 1 Details: the structures are based on a total of 975 are NOE-derived distance constraints, 157 dihedral angle resraints, 39 distance restraints from hydrogen bonds | |||||||||
NMR representative | Selection criteria: minimized average structure | |||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |