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- PDB-7ppm: SHP2 catalytic domain in complex with IRS1 (889-901) phosphopepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ppm | |||||||||
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Title | SHP2 catalytic domain in complex with IRS1 (889-901) phosphopeptide (pSer-892, pTyr-896) | |||||||||
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![]() | SIGNALING PROTEIN / SHP2 / IRS1 / Phosphatase / phosphopeptide / insulin signaling / Insulin receptor substrate 1 | |||||||||
Function / homology | ![]() negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / IRS-related events triggered by IGF1R / genitalia development / atrioventricular canal development / positive regulation of glucose metabolic process / positive regulation of fatty acid beta-oxidation / negative regulation of cell adhesion mediated by integrin ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / IRS-related events triggered by IGF1R / genitalia development / atrioventricular canal development / positive regulation of glucose metabolic process / positive regulation of fatty acid beta-oxidation / negative regulation of cell adhesion mediated by integrin / IRS-mediated signalling / STAT5 Activation / Co-inhibition by BTLA / Netrin mediated repulsion signals / cerebellar cortex formation / negative regulation of neutrophil activation / insulin receptor complex / positive regulation of hormone secretion / Activated NTRK3 signals through PI3K / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of protein export from nucleus / positive regulation of ossification / positive regulation of lipopolysaccharide-mediated signaling pathway / Interleukin-37 signaling / Signaling by Leptin / hormone metabolic process / cellular response to fatty acid / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / negative regulation of chondrocyte differentiation / Signaling by LTK / Signal regulatory protein family interactions / PI3K/AKT activation / face morphogenesis / ERBB signaling pathway / platelet formation / triglyceride metabolic process / megakaryocyte development / organ growth / Signaling by ALK / negative regulation of type I interferon production / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / Co-inhibition by CTLA4 / Platelet sensitization by LDL / STAT5 activation downstream of FLT3 ITD mutants / peptide hormone receptor binding / PI-3K cascade:FGFR2 / IRS activation / PI-3K cascade:FGFR4 / MAPK3 (ERK1) activation / PI-3K cascade:FGFR1 / Prolactin receptor signaling / neurotrophin TRK receptor signaling pathway / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / platelet-derived growth factor receptor signaling pathway / MAPK1 (ERK2) activation / PECAM1 interactions / Bergmann glial cell differentiation / inner ear development / peptidyl-tyrosine dephosphorylation / positive regulation of intracellular signal transduction / phosphoprotein phosphatase activity / RET signaling / Regulation of IFNA/IFNB signaling / non-membrane spanning protein tyrosine phosphatase activity / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / SOS-mediated signalling / Co-inhibition by PD-1 / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / Signal attenuation / ephrin receptor signaling pathway / regulation of protein-containing complex assembly / Activated NTRK2 signals through FRS2 and FRS3 / Regulation of IFNG signaling / Growth hormone receptor signaling / phosphatidylinositol 3-kinase binding / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / GPVI-mediated activation cascade / Signaling by FLT3 ITD and TKD mutants / negative regulation of T cell proliferation / T cell costimulation / hormone-mediated signaling pathway / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / cell adhesion molecule binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / FRS-mediated FGFR1 signaling / Tie2 Signaling / insulin-like growth factor receptor binding / signaling adaptor activity / phosphotyrosine residue binding / FLT3 Signaling Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Sok, P. / Zeke, A. / Remenyi, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling. Authors: Zeke, A. / Takacs, T. / Sok, P. / Nemeth, K. / Kirsch, K. / Egri, P. / Poti, A.L. / Bento, I. / Tusnady, G.E. / Remenyi, A. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() ![]() ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.3 KB | Display | ![]() |
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PDB format | ![]() | 103.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.2 KB | Display | ![]() |
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Full document | ![]() | 455.3 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pplC ![]() 7ppnC ![]() 3zm0S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 32629.900 Da / Num. of mol.: 1 / Mutation: catalytic inactivation: C213S Source method: isolated from a genetically manipulated source Details: SHP2 catalytic domain was optimised for crystallisation and missing residues from 315 to 323 (original SHP2 sequence numbering), these missing residues in the optimised construct (74-77) ...Details: SHP2 catalytic domain was optimised for crystallisation and missing residues from 315 to 323 (original SHP2 sequence numbering), these missing residues in the optimised construct (74-77) were replaced to GSSG resideues.,SHP2 catalytic domain was optimised for crystallisation and missing residues from 315 to 323 (original SHP2 sequence numbering), these missing residues in the optimised construct (74-77) were replaced to GSSG resideues. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1669.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Phosphorylated residues: pSer-892, pTyr-896 / Source: (synth.) ![]() |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.07 % / Description: rhomboid shaped crystals |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10% PEG 20000, 100mM Citrate buffer pH 5.5, EDTA 50mM |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen gas cryostream / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→46.05 Å / Num. obs: 56601 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.012 / Rrim(I) all: 0.042 / Net I/σ(I): 26.9 / Num. measured all: 754810 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ZM0 Resolution: 1.48→46.05 Å / SU ML: 0.1614 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5554 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.48→46.05 Å
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Refine LS restraints |
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LS refinement shell |
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