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Yorodumi- PDB-3ojv: Crystal Structure of FGF1 complexed with the ectodomain of FGFR1c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ojv | |||||||||
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Title | Crystal Structure of FGF1 complexed with the ectodomain of FGFR1c exhibiting an ordered ligand specificity-determining betaC'-betaE loop | |||||||||
Components |
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Keywords | Cytokine/Signaling Protein / beta trefoil motif / immunoglobulin-like domain / growth factor / growth factor receptor / extracellular / Cytokine-Signaling Protein 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 / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification ...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 / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / 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 / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / mesonephric epithelium development / branch elongation involved in ureteric bud branching / receptor-receptor interaction / regulation of endothelial tube morphogenesis / response to sodium phosphate / FGFR3b ligand binding and activation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / regulation of endothelial cell chemotaxis to fibroblast growth factor / Epithelial-Mesenchymal Transition (EMT) during gastrulation / 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 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / paraxial mesoderm development / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / 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 / 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 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / phosphatidylinositol-mediated signaling / positive regulation of hepatocyte proliferation / outer ear morphogenesis / middle ear morphogenesis / S100 protein binding / embryonic limb morphogenesis / skeletal system morphogenesis / positive regulation of intracellular signal transduction / ureteric bud development / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / midbrain development / PI-3K cascade:FGFR3 / fibroblast growth factor binding / positive regulation of stem cell proliferation / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / Formation of paraxial mesoderm / PI-3K cascade:FGFR4 / regulation of cell differentiation / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / epithelial to mesenchymal transition / anatomical structure morphogenesis / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / positive regulation of phospholipase C activity / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / cell maturation / FRS-mediated FGFR2 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Hsp70 protein binding / Signaling by FGFR2 in disease / positive regulation of neuron differentiation / extracellular matrix / Signaling by FGFR1 in disease Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Beenken, A. / Mohammadi, M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Plasticity in Interactions of Fibroblast Growth Factor 1 (FGF1) N Terminus with FGF Receptors Underlies Promiscuity of FGF1. Authors: Beenken, A. / Eliseenkova, A.V. / Ibrahimi, O.A. / Olsen, S.K. / Mohammadi, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ojv.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ojv.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ojv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/3ojv ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3ojv | HTTPS FTP |
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-Related structure data
Related structure data | 3oj2C 3ojmC 1evtS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15420.397 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P05230 #2: Protein | Mass: 25375.973 Da / Num. of mol.: 2 / Fragment: FGFR1c / Mutation: N185Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFBR, FGFR1, FLG, FLT2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 References: UniProt: P11362, receptor protein-tyrosine kinase #3: Polysaccharide | 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: 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: 2.55 Å3/Da / Density % sol: 51.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, 15% PEG4000, 0.1M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 173 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97912 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2005 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. all: 24626 / Num. obs: 24626 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.064 / Net I/σ(I): 16.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EVT Resolution: 2.6→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: There is substantial electron density in the difference Fourier synthesis (Fo - Fc) map contoured at 1 sigma level between the heparin binding sites of the two FGFs. The shape of the ...Details: There is substantial electron density in the difference Fourier synthesis (Fo - Fc) map contoured at 1 sigma level between the heparin binding sites of the two FGFs. The shape of the electron density and its location (sandwiched between heparin binding sites of the two FGFs) clearly indicate that it belongs to the cocrystallized heparin octasaccharide. However, only six monosaccharides of the octasacchride could be confidently built into this density. Importantly, there are densities of the size of a disaccharide unit at either end of this modeled hexasaccharide suggesting that the hexasaccharide could be translated by two sugar units along its helical axis. This observation suggests that the octasaccharide does not bind in a fixed fashion to the FGFs and can glide by two sugar units along its axis. As a result, the temperature factor and the real space R factor for the octasaccharide are abnormally high.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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Refine LS restraints |
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LS refinement shell |
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