+Open data
-Basic information
Entry | Database: PDB / ID: 3kxx | ||||||
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Title | Structure of the mutant Fibroblast Growth Factor receptor 1 | ||||||
Components | Basic fibroblast growth factor receptor 1 | ||||||
Keywords | TRANSFERASE / kinase / RTK / interface / phosphorylation / Alternative splicing / ATP-binding / Chromosomal rearrangement / Craniosynostosis / Disease mutation / Disulfide bond / Dwarfism / Glycoprotein / Heparin-binding / Hypogonadotropic hypogonadism / Immunoglobulin domain / Kallmann syndrome / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Receptor / Transmembrane / Tyrosine-protein kinase | ||||||
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 / vitamin D3 metabolic process / FGFR1c and Klotho ligand binding and activation / 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 / vitamin D3 metabolic process / FGFR1c and Klotho ligand binding and activation / 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 / 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 / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / 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 / cellular response to fibroblast growth factor stimulus / outer ear morphogenesis / middle ear morphogenesis / 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 / regulation of cell differentiation / positive regulation of stem cell proliferation / fibroblast growth factor binding / Formation of paraxial mesoderm / PI-3K cascade:FGFR1 / phosphatidylinositol-mediated signaling / cell maturation / PI3K Cascade / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / : / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / positive regulation of cardiac muscle cell proliferation / Signal transduction by L1 / FRS-mediated FGFR1 signaling / Signaling by FGFR1 in disease / positive regulation of neuron differentiation / NCAM signaling for neurite out-growth / SH2 domain binding / positive regulation of MAP kinase activity / stem cell proliferation / skeletal system development / stem cell differentiation / receptor protein-tyrosine kinase / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / neuron migration / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of neuron projection development / MAPK cascade / PIP3 activates AKT signaling / neuron projection development / cell migration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / heparin binding / RAF/MAP kinase cascade / gene expression / protein tyrosine kinase activity / cytoplasmic vesicle / angiogenesis / protein autophosphorylation / in utero embryonic development / receptor complex / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Bae, J.H. / Boggon, T.J. / Tome, F. / Mandiyan, V. / Lax, I. / Schlessinger, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Asymmetric receptor contact is required for tyrosine autophosphorylation of fibroblast growth factor receptor in living cells. Authors: Bae, J.H. / Boggon, T.J. / Tome, F. / Mandiyan, V. / Lax, I. / Schlessinger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kxx.cif.gz | 235.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kxx.ent.gz | 192.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kxx_validation.pdf.gz | 446.2 KB | Display | wwPDB validaton report |
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Full document | 3kxx_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 3kxx_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 3kxx_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/3kxx ftp://data.pdbj.org/pub/pdb/validation_reports/kx/3kxx | HTTPS FTP |
-Related structure data
Related structure data | 3ky2C 1fgkS 3gqiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 36198.523 Da / Num. of mol.: 4 / Fragment: Kinase domain (UNP residues 458 to 765) / Mutation: C488A, R577E, C584S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, FGFBR, FLG, FLT2 / Production host: Escherichia coli (E. coli) References: UniProt: P11362, receptor protein-tyrosine kinase |
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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: 3.23 Å3/Da / Density % sol: 61.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Crystals were grown at room temperature in 14 days using the hanging drop technique containing equal volumes of protein solution and reservoir buffer (15 % [w/v] polyethylene glycol 3350, ...Details: Crystals were grown at room temperature in 14 days using the hanging drop technique containing equal volumes of protein solution and reservoir buffer (15 % [w/v] polyethylene glycol 3350, 200 mM lithium citrate). , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2009 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 30954 / Num. obs: 30692 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.358 / Num. unique all: 3028 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1FGK, 3GQI Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.2→50 Å
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Refine LS restraints |
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