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Yorodumi- PDB-3qs7: Crystal structure of a human Flt3 ligand-receptor ternary complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qs7 | ||||||
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Title | Crystal structure of a human Flt3 ligand-receptor ternary complex | ||||||
Components |
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Keywords | CYTOKINE/SIGNALING PROTEIN / immunoglobulin-like domain / four-helical bundle cytokine / cytokine-receptor complex / extracellular complex / receptor tyrosine kinase / CYTOKINE-SIGNALING PROTEIN complex | ||||||
Function / homology | Function and homology information 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 / nuclear glucocorticoid receptor binding / phosphatidylinositol 3-kinase activator activity / STAT5 Activation / myeloid progenitor cell differentiation / FLT3 signaling through SRC family kinases / cellular response to glucocorticoid stimulus / cytokine receptor activity / embryonic hemopoiesis / STAT5 activation downstream of FLT3 ITD mutants / cellular response to cytokine stimulus / growth factor binding / 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 / 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 tyrosine kinase binding / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / : / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / regulation of apoptotic process / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.3 Å | ||||||
Authors | Verstraete, K. / Savvides, S.N. | ||||||
Citation | Journal: Blood / Year: 2011 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: Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qs7.cif.gz | 281.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qs7.ent.gz | 211.4 KB | Display | PDB format |
PDBx/mmJSON format | 3qs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/3qs7 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qs7 | HTTPS FTP |
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-Related structure data
Related structure data | 3qs9C 1eteS 2e9wS 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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2 |
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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.) Homo sapiens (human) / Gene: FLT3LG / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA-GAMI(DE3) / References: UniProt: P49771 #2: Protein | Mass: 48099.188 Da / Num. of mol.: 4 / Fragment: extracellular domain (UNP residues 27-436) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FLT3, STK1 / Plasmid: pcDNA4/TO / Cell line (production host): HEK 293 GNTI- / Production host: Homo sapiens (human) References: UniProt: P36888, receptor protein-tyrosine kinase #3: Sugar | ChemComp-NAG / |
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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: 2.96 Å3/Da / Density % sol: 58.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 11-13% PEG4000, 0.1 M magnesium chloride, 50 mM MES, 5 mg/mL Flt3 ligand-receptor complex, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9714 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9714 Å / Relative weight: 1 |
Reflection | Resolution: 4.3→40 Å / Num. all: 20434 / Num. obs: 20184 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 135 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 12.04 |
Reflection shell | Resolution: 4.3→4.45 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.08 / % possible all: 98.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1ETE AND 2E9W Resolution: 4.3→39.04 Å / Cor.coef. Fo:Fc: 0.8832 / Cor.coef. Fo:Fc free: 0.8516 / 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: 242.95 Å2 / Biso mean: 168.8768 Å2 / Biso min: 122.08 Å2
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Refine analyze | Luzzati coordinate error obs: 1.374 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.3→39.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.3→4.53 Å / Total num. of bins used: 10
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