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- PDB-3qs9: Crystal structure of a human Flt3 ligand-receptor ternary complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 3qs9 | ||||||
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Title | Crystal structure of a human Flt3 ligand-receptor ternary complex | ||||||
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![]() | CYTOKINE/SIGNALING PROTEIN / immunoglobulin-like domain / four-helical bundle cytokine / hematopoietic cytokine-receptor complex / cell surface / extracellular complex / receptor tyrosine kinase / CYTOKINE-SIGNALING PROTEIN complex | ||||||
Function / homology | ![]() FLT3 mutants bind TKIs / KW2449-resistant FLT3 mutants / semaxanib-resistant FLT3 mutants / crenolanib-resistant FLT3 mutants / gilteritinib-resistant FLT3 mutants / lestaurtinib-resistant FLT3 mutants / midostaurin-resistant FLT3 mutants / pexidartinib-resistant FLT3 mutants / ponatinib-resistant FLT3 mutants / quizartinib-resistant FLT3 mutants ...FLT3 mutants bind TKIs / KW2449-resistant FLT3 mutants / semaxanib-resistant FLT3 mutants / crenolanib-resistant FLT3 mutants / gilteritinib-resistant FLT3 mutants / lestaurtinib-resistant FLT3 mutants / midostaurin-resistant FLT3 mutants / pexidartinib-resistant FLT3 mutants / ponatinib-resistant FLT3 mutants / quizartinib-resistant FLT3 mutants / sorafenib-resistant FLT3 mutants / sunitinib-resistant FLT3 mutants / tandutinib-resistant FLT3 mutants / linifanib-resistant FLT3 mutants / tamatinib-resistant FLT3 mutants / leukocyte homeostasis / lymphocyte proliferation / pro-B cell differentiation / common myeloid progenitor cell proliferation / dendritic cell differentiation / vascular endothelial growth factor receptor activity / phosphatidylinositol 3-kinase activator activity / STAT5 Activation / nuclear glucocorticoid receptor binding / myeloid progenitor cell differentiation / FLT3 signaling through SRC family kinases / cellular response to glucocorticoid stimulus / embryonic hemopoiesis / cytokine receptor activity / STAT5 activation downstream of FLT3 ITD mutants / growth factor binding / cellular response to cytokine stimulus / hemopoiesis / PI3K Cascade / animal organ regeneration / Signaling by FLT3 ITD and TKD mutants / positive regulation of tyrosine phosphorylation of STAT protein / FLT3 signaling by CBL mutants / cell surface receptor protein tyrosine kinase signaling pathway / response to organonitrogen compound / Negative regulation of FLT3 / FLT3 Signaling / transmembrane receptor protein tyrosine kinase activity / B cell differentiation / cytokine activity / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / : / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / regulation of apoptotic process / protein tyrosine kinase activity / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome membrane / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / protein-containing complex binding / cell surface / endoplasmic reticulum / signal transduction / extracellular space / extracellular region / ATP binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Verstraete, K. / Savvides, S.N. | ||||||
![]() | ![]() Title: Structural insights into the extracellular assembly of the hematopoietic Flt3 signaling complex. Authors: Verstraete, K. / Vandriessche, G. / Januar, M. / Elegheert, J. / Shkumatov, A.V. / Desfosses, A. / Van Craenenbroeck, K. / Svergun, D.I. / Gutsche, I. / Vergauwen, B. / Savvides, S.N. #1: ![]() Title: Inducible production of human Flt3 ectodomain variants in mammalian cells and preliminary crystallographic analysis of Flt3 ligand-receptor complexes Authors: Verstraete, K. / Vandriessche, G. / Januar, M. / Elegheert, J. / Shkumatov, A. / Desfosses, A. / Van Craenenbroeck, K. / Svergun, D. / Gutsche, I. / Vergauwen, B. / Savvides, S.N. #2: Journal: Protein J. / Year: 2009 Title: Efficient production of bioactive recombinant human Flt3 ligand in E. coli. Authors: Verstraete, K. / Koch, S. / Ertugrul, S. / Vandenberghe, I. / Aerts, M. / Vandriessche, G. / Thiede, C. / Savvides, S.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 341 KB | Display | ![]() |
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PDB format | ![]() | 249.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.7 KB | Display | ![]() |
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Full document | ![]() | 496.6 KB | Display | |
Data in XML | ![]() | 38.6 KB | Display | |
Data in CIF | ![]() | 59.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3qs7SC ![]() 1eteS ![]() 2e9wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15873.217 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 27-160) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 59534.137 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 27-540) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P36888, receptor protein-tyrosine kinase |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.24 Å3/Da / Density % sol: 70.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 12-14% w/v PEG3350, 0.2 M lithium citrate, 0.1 M TRIS-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0762 Å / Relative weight: 1 |
Reflection | Resolution: 7.8→35 Å / Num. all: 5853 / Num. obs: 5656 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.38 % / Biso Wilson estimate: 401 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 9.08 |
Reflection shell | Resolution: 7.8→8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.9 / % possible all: 92.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1ETE,2E9W,3QS7 Resolution: 7.8→35 Å / Cor.coef. Fo:Fc: 0.7108 / Cor.coef. Fo:Fc free: 0.611 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 469.34 Å2 / Biso mean: 363.75 Å2 / Biso min: 288.74 Å2
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Refine analyze | Luzzati coordinate error obs: 2.415 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 7.8→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 7.8→8.72 Å / Total num. of bins used: 5
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