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Yorodumi- PDB-1evt: CRYSTAL STRUCTURE OF FGF1 IN COMPLEX WITH THE EXTRACELLULAR LIGAN... -
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-Basic information
Entry | Database: PDB / ID: 1evt | ||||||
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Title | CRYSTAL STRUCTURE OF FGF1 IN COMPLEX WITH THE EXTRACELLULAR LIGAND BINDING DOMAIN OF FGF RECEPTOR 1 (FGFR1) | ||||||
Components |
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Keywords | GROWTH FACTOR/GROWTH FACTOR RECEPTOR / IMMUNOGLOBULIN (IG) LIKE DOMAINS BELONGING TO THE I-SET SUBGROUP WITHIN IG-LIKE DOMAINS / B-TREFOIL FOLD / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / Signaling by plasma membrane FGFR1 fusions / ventricular zone neuroblast division / diphosphate metabolic process / vitamin D3 metabolic process / regulation of phosphate transport ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / Signaling by plasma membrane FGFR1 fusions / ventricular zone neuroblast division / diphosphate metabolic process / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / response to sodium phosphate / FGFR2b ligand binding and activation / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / auditory receptor cell development / Epithelial-Mesenchymal Transition (EMT) during gastrulation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / chordate embryonic development / Phospholipase C-mediated cascade; FGFR2 / fibroblast growth factor receptor activity / positive regulation of parathyroid hormone secretion / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade; FGFR3 / positive regulation of phospholipase activity / mesenchymal cell proliferation / positive regulation of cholesterol biosynthetic process / paraxial mesoderm development / fibroblast growth factor receptor binding / lung-associated mesenchyme development / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / cell projection assembly / S100 protein binding / cellular response to fibroblast growth factor stimulus / positive regulation of hepatocyte proliferation / skeletal system morphogenesis / outer ear morphogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / middle ear morphogenesis / positive regulation of intracellular signal transduction / embryonic limb morphogenesis / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / midbrain development / cardiac muscle cell proliferation / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / fibroblast growth factor binding / regulation of cell differentiation / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / positive regulation of stem cell proliferation / PI-3K cascade:FGFR1 / Formation of paraxial mesoderm / phosphatidylinositol-mediated signaling / positive regulation of cell division / PI3K Cascade / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / anatomical structure morphogenesis / chondrocyte differentiation / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR4 / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR3 signaling / cell maturation / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / positive regulation of neuron differentiation / Hsp70 protein binding / Signaling by FGFR1 in disease / activation of protein kinase B activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å | ||||||
Authors | Plotnikov, A.N. / Hubbard, S.R. / Schlessinger, J. / Mohammadi, M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2000 Title: Crystal structures of two FGF-FGFR complexes reveal the determinants of ligand-receptor specificity. Authors: Plotnikov, A.N. / Hubbard, S.R. / Schlessinger, 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 | 1evt.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1evt.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 1evt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1evt_validation.pdf.gz | 398.8 KB | Display | wwPDB validaton report |
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Full document | 1evt_full_validation.pdf.gz | 419.2 KB | Display | |
Data in XML | 1evt_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1evt_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1evt ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1evt | HTTPS FTP |
-Related 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: 15232.148 Da / Num. of mol.: 2 Fragment: THE B-TREFOIL CORE OF FIBROBLAST GROWTH FACTOR 1 (FGF1) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / References: UniProt: P05230 #2: Protein | Mass: 25260.777 Da / Num. of mol.: 2 Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN OF FGF RECEPTOR 1 (FGFR1) CONSISTING OF IMMUNOGLOBULIN LIKE DOMAINS II (D2) AND III (D3) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / References: UniProt: P11362 #3: Chemical | ChemComp-SO4 / |
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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: 2.92 Å3/Da / Density % sol: 57.82 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG 4000, Isopropanol, HEPES-NaOH, pH 7.5, VAPOR DIFFUSION, temperature 298.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9794 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. obs: 49288 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.226 / % possible all: 90.5 |
Reflection | *PLUS Num. obs: 22330 / Num. measured all: 49288 |
Reflection shell | *PLUS % possible obs: 90.5 % |
-Processing
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Refinement | Resolution: 2.8→25 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: CNS / Bsol: 27.76 Å2 / ksol: 0.342 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.8→25 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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