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Yorodumi- PDB-4gl9: Crystal structure of inhibitory protein SOCS3 in complex with JAK... -
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-Basic information
Entry | Database: PDB / ID: 4gl9 | ||||||
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Title | Crystal structure of inhibitory protein SOCS3 in complex with JAK2 kinase domain and fragment of GP130 intracellular domain | ||||||
Components |
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Keywords | transferase/transferase inhibitor / kinase inhibitor receptor cytokine signalling / phosphorylation / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information response to granulocyte macrophage colony-stimulating factor / IFNG signaling activates MAPKs / positive regulation of cell activation / Regulation of IFNG signaling / : / PTK6 Activates STAT3 / Signaling by Erythropoietin / Growth hormone receptor signaling / Interleukin-4 and Interleukin-13 signaling / oncostatin-M receptor activity ...response to granulocyte macrophage colony-stimulating factor / IFNG signaling activates MAPKs / positive regulation of cell activation / Regulation of IFNG signaling / : / PTK6 Activates STAT3 / Signaling by Erythropoietin / Growth hormone receptor signaling / Interleukin-4 and Interleukin-13 signaling / oncostatin-M receptor activity / Interleukin-12 signaling / Prolactin receptor signaling / IL-6-type cytokine receptor ligand interactions / Interleukin-23 signaling / Interleukin-20 family signaling / leukemia inhibitory factor receptor activity / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Interferon gamma signaling / Interleukin-27 signaling / Signaling by CSF3 (G-CSF) / Erythropoietin activates RAS / interleukin-6 receptor activity / triglyceride mobilization / interleukin-6 binding / Interleukin-6 signaling / Interleukin-35 Signalling / oncostatin-M receptor complex / Interferon alpha/beta signaling / oncostatin-M-mediated signaling pathway / Inactivation of CSF3 (G-CSF) signaling / ciliary neurotrophic factor receptor activity / ciliary neurotrophic factor receptor binding / negative regulation of interleukin-6-mediated signaling pathway / leukemia inhibitory factor signaling pathway / Signaling by SCF-KIT / ciliary neurotrophic factor receptor complex / RAF activation / interleukin-27-mediated signaling pathway / ciliary neurotrophic factor-mediated signaling pathway / interleukin-6 receptor complex / Cyclin D associated events in G1 / RAF/MAP kinase cascade / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / : / Interleukin receptor SHC signaling / interleukin-6 receptor binding / regulation of Notch signaling pathway / interleukin-11-mediated signaling pathway / cellular response to interleukin-17 / negative regulation of tyrosine phosphorylation of STAT protein / negative regulation of heart contraction / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / Factors involved in megakaryocyte development and platelet production / mineralocorticoid receptor signaling pathway / histone H3Y41 kinase activity / activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of growth factor dependent skeletal muscle satellite cell proliferation / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of astrocyte differentiation / symbiont-induced defense-related programmed cell death / Neddylation / mammary gland epithelium development / regulation of postsynapse to nucleus signaling pathway / positive regulation of growth hormone receptor signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / protein tyrosine kinase inhibitor activity / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / negative regulation of receptor signaling pathway via JAK-STAT / intestinal epithelial cell development / interleukin-12 receptor binding / post-embryonic hemopoiesis / collagen-activated signaling pathway / interleukin-5-mediated signaling pathway / response to interleukin-12 / 1-phosphatidylinositol-3-kinase regulator activity / myeloid cell differentiation / positive regulation of leukocyte proliferation / activation of Janus kinase activity / interleukin-12 receptor complex / interleukin-23 receptor complex / positive regulation of platelet aggregation / tyrosine phosphorylation of STAT protein / positive regulation of platelet activation / postsynapse to nucleus signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of T-helper 17 type immune response / type 1 angiotensin receptor binding / positive regulation of NK T cell proliferation / regulation of nitric oxide biosynthetic process / acetylcholine receptor binding / interleukin-12-mediated signaling pathway / interleukin-3-mediated signaling pathway / cellular response to interleukin-3 / phosphatidylinositol 3-kinase complex / miRNA binding / positive regulation of signaling receptor activity / cytokine receptor activity Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Kershaw, N.J. / Murphy, J.M. / Laktyushin, A. / Nicola, N.A. / Babon, J.J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: SOCS3 binds specific receptor-JAK complexes to control cytokine signaling by direct kinase inhibition. Authors: Kershaw, N.J. / Murphy, J.M. / Liau, N.P. / Varghese, L.N. / Laktyushin, A. / Whitlock, E.L. / Lucet, I.S. / Nicola, N.A. / Babon, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gl9.cif.gz | 341.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gl9.ent.gz | 289.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/4gl9 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/4gl9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35111.883 Da / Num. of mol.: 4 / Fragment: Kinase domain (unp residues 836-1132) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Jak2, mCG_9104 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: G5E852, UniProt: Q62120*PLUS, non-specific protein-tyrosine kinase #2: Protein/peptide | Mass: 1605.573 Da / Num. of mol.: 4 / Fragment: unp residues 750-764 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q00560 #3: Protein | Mass: 15641.506 Da / Num. of mol.: 4 Fragment: chimeric fusion of Intracellular domain (unp residues 22-128 and 163-185) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Socs3, Cis3, Cish3 / Production host: Escherichia coli (E. coli) / References: UniProt: O35718 #4: Chemical | ChemComp-IZA / #5: Chemical | ChemComp-PO4 / | |
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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: 4.23 Å3/Da / Density % sol: 70.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.33M di-potassium hydrogen phosphate, 1.67M sodium dihydrogen phosphate, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95371 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95371 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→45.584 Å / Num. obs: 31617 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→45.58 Å / σ(F): 1.99 / Phase error: 36.69 / Stereochemistry target values: TWIN_LSQ_F
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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: 3.9→45.58 Å
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Refine LS restraints |
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LS refinement shell |
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