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- PDB-7ppn: SHP2 catalytic domain in complex with CD28 (183-198) phosphopepti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ppn | |||||||||
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Title | SHP2 catalytic domain in complex with CD28 (183-198) phosphopeptide (pTyr-191, p-Thr-195) | |||||||||
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![]() | SIGNALING PROTEIN / SHP2 / Phosphatase / CD28 / phosphopeptide / signaling | |||||||||
Function / homology | ![]() Nef mediated downregulation of CD28 cell surface expression / regulatory T cell differentiation / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development ...Nef mediated downregulation of CD28 cell surface expression / regulatory T cell differentiation / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of hormone secretion / cerebellar cortex formation / CD28 co-stimulation / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / Signaling by Leptin / negative regulation of chondrocyte differentiation / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / face morphogenesis / ERBB signaling pathway / Costimulation by the CD28 family / CD28 dependent Vav1 pathway / Signal regulatory protein family interactions / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / triglyceride metabolic process / CTLA4 inhibitory signaling / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / positive regulation of interleukin-4 production / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / positive regulation of interleukin-10 production / phosphoprotein phosphatase activity / inner ear development / neurotrophin TRK receptor signaling pathway / humoral immune response / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / immunological synapse / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / PD-1 signaling / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / positive regulation of viral genome replication / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of insulin secretion / coreceptor activity / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Tie2 Signaling / FRS-mediated FGFR1 signaling / cellular response to epidermal growth factor stimulus / cell adhesion molecule binding / GPVI-mediated activation cascade / T cell costimulation / positive regulation of interleukin-2 production / T cell activation / FLT3 Signaling / positive regulation of interferon-beta production 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. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.9 KB | Display | ![]() |
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PDB format | ![]() | 104.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.4 KB | Display | ![]() |
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Full document | ![]() | 449.3 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pplC ![]() 7ppmC ![]() 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: 2198.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Phosphorylated residues: pTyr-191, p-Thr-195 / Source: (synth.) ![]() |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.03 % / Description: rhomboid shaped crystal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10% PEG 20000, 100 mM Citrate buffer pH 5.5, 50 mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: N gas cryosteam / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 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: 1.9→49.25 Å / Num. obs: 26486 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.014 / Rrim(I) all: 0.05 / Net I/σ(I): 26.1 / Num. measured all: 341960 | ||||||||||||||||||||||||||||||
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: 1.9→45.27 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3602 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: 52.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→45.27 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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