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Yorodumi- PDB-5w21: Crystal Structure of a 1:1:1 FGF23-FGFR1c-aKlotho Ternary Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w21 | ||||||
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Title | Crystal Structure of a 1:1:1 FGF23-FGFR1c-aKlotho Ternary Complex | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN BINDING / complex / ligand / receptor / co-receptor / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / norepinephrine biosynthetic process / positive regulation of vitamin D 24-hydroxylase activity / beta-glucuronidase / 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 / Signaling by plasma membrane FGFR1 fusions ...type 1 fibroblast growth factor receptor binding / FGFRL1 modulation of FGFR1 signaling / norepinephrine biosynthetic process / positive regulation of vitamin D 24-hydroxylase activity / beta-glucuronidase / 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 / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / negative regulation of hormone secretion / vitamin D3 metabolic process / FGFR1c and Klotho ligand binding and activation / beta-glucuronidase activity / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / intracellular phosphate ion homeostasis / vitamin D catabolic process / response to sodium phosphate / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / negative regulation of bone mineralization / phosphate ion homeostasis / positive regulation of parathyroid hormone secretion / chordate embryonic development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation / paraxial mesoderm development / fibroblast growth factor receptor binding / cellular response to vitamin D / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / vitamin D binding / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / branching involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / energy reserve metabolic process / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / response to vitamin D / cellular response to leptin stimulus / cellular response to interleukin-6 / cell projection assembly / negative regulation of systemic arterial blood pressure / cellular response to fibroblast growth factor stimulus / response to angiotensin / outer ear morphogenesis / middle ear morphogenesis / cellular response to parathyroid hormone stimulus / embryonic limb morphogenesis / skeletal system morphogenesis / positive regulation of vascular endothelial cell proliferation / cardiac muscle cell proliferation / positive regulation of mesenchymal cell proliferation / positive regulation of endothelial cell chemotaxis / ureteric bud development / inner ear morphogenesis / midbrain development / beta-glucosidase activity / PI-3K cascade:FGFR3 / regulation of cell differentiation / PI-3K cascade:FGFR2 / positive regulation of stem cell proliferation / fibroblast growth factor binding / PI-3K cascade:FGFR4 / Formation of paraxial mesoderm / PI-3K cascade:FGFR1 / phosphatidylinositol-mediated signaling / response to magnesium ion / PI3K Cascade / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / negative regulation of osteoblast differentiation / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / positive regulation of bone mineralization / SHC-mediated cascade:FGFR3 / : / SHC-mediated cascade:FGFR2 / calcium ion homeostasis / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Mohammadi, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nature / Year: 2018 Title: alpha-Klotho is a non-enzymatic molecular scaffold for FGF23 hormone signalling. Authors: Chen, G. / Liu, Y. / Goetz, R. / Fu, L. / Jayaraman, S. / Hu, M.C. / Moe, O.W. / Liang, G. / Li, X. / Mohammadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w21.cif.gz | 558.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w21.ent.gz | 459.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/5w21 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/5w21 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Fibroblast growth factor ... , 2 types, 2 molecules BC
#2: Protein | Mass: 25406.482 Da / Num. of mol.: 1 / Fragment: UNP residues 25-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF23, HYPF, UNQ3027/PRO9828 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZV9 |
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#3: Protein | Mass: 25375.973 Da / Num. of mol.: 1 / Fragment: D2 and D3 region (UNP residues 142-365) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR / Production host: Escherichia coli (E. coli) References: UniProt: P11362, receptor protein-tyrosine kinase |
-Protein / Sugars , 2 types, 8 molecules A
#1: Protein | Mass: 112666.109 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 1-981) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KL / Production host: Homo sapiens (human) / References: UniProt: Q9UEF7, beta-glucuronidase |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 2 molecules
#5: Chemical | ChemComp-ZN / |
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#6: 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: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 22% PEG350 MME, 0.1 M Tris-HCl, pH 8.0, 1 mM reduced glutathione, 1 mM oxidized glutathione |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2016 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 58000 / % possible obs: 99.7 % / Redundancy: 7.5 % / Net I/σ(I): 11.1 |
Reflection shell | Highest resolution: 3 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 2P39, 1CVS , & 2DGA Resolution: 3→48.801 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.6 / 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: 3→48.801 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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