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Yorodumi- PDB-1iil: CRYSTAL STRUCTURE OF PRO253ARG APERT MUTANT FGF RECEPTOR 2 (FGFR2... -
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-Basic information
Entry | Database: PDB / ID: 1iil | ||||||
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Title | CRYSTAL STRUCTURE OF PRO253ARG APERT MUTANT FGF RECEPTOR 2 (FGFR2) IN COMPLEX WITH FGF2 | ||||||
Components |
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Keywords | GROWTH FACTOR/GROWTH FACTOR RECEPTOR / IMMUNOGLOBULIN LIKE DOMAIN / B-TREFOIL / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / 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 / lymphatic endothelial cell migration / chemokine binding / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / negative regulation of fibroblast growth factor receptor signaling pathway / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / embryonic organ morphogenesis / positive regulation of cerebellar granule cell precursor proliferation / endochondral bone growth / morphogenesis of embryonic epithelium / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / epidermis morphogenesis / bud elongation involved in lung branching / cerebellar granule cell precursor proliferation / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / receptor-receptor interaction / membranous septum morphogenesis / positive regulation of stem cell differentiation / reproductive structure development / limb bud formation / lung lobe morphogenesis / hyaluronan catabolic process / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / glial cell differentiation / ventricular zone neuroblast division / regulation of endothelial cell chemotaxis to fibroblast growth factor / embryonic digestive tract morphogenesis / inner ear auditory receptor cell differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / negative regulation of wound healing / mesenchymal cell differentiation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / stem cell development / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / Phospholipase C-mediated cascade; FGFR3 / branching involved in labyrinthine layer morphogenesis / embryonic morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / positive regulation of epithelial tube formation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / embryonic pattern specification / Signaling by activated point mutants of FGFR1 / outflow tract septum morphogenesis / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / paracrine signaling / mesodermal cell differentiation / digestive tract development / negative regulation of fibroblast migration / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / positive regulation of endothelial cell chemotaxis Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Ibrahimi, O.A. / Eliseenkova, A.V. / Plotnikov, A.N. / Ornitz, D.M. / Mohammadi, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Structural basis for fibroblast growth factor receptor 2 activation in Apert syndrome. Authors: Ibrahimi, O.A. / Eliseenkova, A.V. / Plotnikov, A.N. / Yu, K. / Ornitz, D.M. / Mohammadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iil.cif.gz | 270 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iil.ent.gz | 217.2 KB | Display | PDB format |
PDBx/mmJSON format | 1iil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/1iil ftp://data.pdbj.org/pub/pdb/validation_reports/ii/1iil | HTTPS FTP |
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-Related structure data
Related structure data | 1ii4C 1ev2S 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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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 17249.732 Da / Num. of mol.: 4 / Mutation: C78S,C96S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09038 #2: Protein | Mass: 24701.012 Da / Num. of mol.: 4 Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN CONSISTING OF IG-LIKE DOMAINS II (D2) AND III (D3), RESIDUES 147-366 Mutation: P253R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21802, EC: 2.7.1.112 #3: 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: 2.75 Å3/Da / Density % sol: 55.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Isopropanol, HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97624 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 321836 / Num. obs: 321836 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.137 / % possible all: 95.9 |
Reflection | *PLUS Num. obs: 85442 / Num. measured all: 321836 |
Reflection shell | *PLUS % possible obs: 95.9 % |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EV2 Resolution: 2.3→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS / Bsol: 32.5 Å2 / ksol: 0.352 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 4.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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