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Yorodumi- PDB-4h34: Crystal structure of the tyrosine phosphatase SHP-2 with Q506P mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h34 | ||||||
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Title | Crystal structure of the tyrosine phosphatase SHP-2 with Q506P mutation | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 11 | ||||||
Keywords | HYDROLASE / alpha/beta proteins / SH2 domain / phosphatase domain / Tyrosine Phosphatase SHP-2 | ||||||
Function / homology | Function and homology information negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of hormone secretion ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of hormone secretion / cerebellar cortex formation / 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 / Signal regulatory protein family interactions / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / CTLA4 inhibitory signaling / triglyceride metabolic process / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / 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 / PECAM1 interactions / MAPK1 (ERK2) activation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / Bergmann glial cell differentiation / phosphoprotein phosphatase activity / inner ear development / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / 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 / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of insulin secretion / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / 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 / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / Downstream signal transduction / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine kinase binding / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / positive regulation of glucose import / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / insulin receptor binding / epidermal growth factor receptor signaling pathway / multicellular organism growth Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Qiu, W. / Lin, A. / Hutchinson, A. / Romanov, V. / Ruzanov, M. / Thompson, C. / Lam, K. / Kisselman, G. / Battaile, K. / Chirgadze, N.Y. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the tyrosine phosphatase SHP-2 with Q506P mutation Authors: Qiu, W. / Lin, A. / Hutchinson, A. / Romanov, V. / Ruzanov, M. / Thompson, C. / Lam, K. / Kisselman, G. / Battaile, K. / Chirgadze, N.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h34.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h34.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 4h34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h34_validation.pdf.gz | 459.4 KB | Display | wwPDB validaton report |
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Full document | 4h34_full_validation.pdf.gz | 463.7 KB | Display | |
Data in XML | 4h34_validation.xml.gz | 19 KB | Display | |
Data in CIF | 4h34_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/4h34 ftp://data.pdbj.org/pub/pdb/validation_reports/h3/4h34 | HTTPS FTP |
-Related structure data
Related structure data | 2shpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64408.574 Da / Num. of mol.: 1 / Fragment: N-SH2, C-SH2 and Phosphatase domain / Mutation: Q506P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06124, protein-tyrosine-phosphatase | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: 0.02M DDT, 0.1M Tris pH8.0, 19% PEG4000, 10% Glycerol, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2011 |
Radiation | Monochromator: Si-111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 14356 / Num. obs: 14342 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.45 % / Biso Wilson estimate: 53.56 Å2 / Rmerge(I) obs: 0.1386 / Net I/σ(I): 12.05 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.25 % / Rmerge(I) obs: 0.5595 / Mean I/σ(I) obs: 2.81 / Num. unique all: 1449 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2SHP Resolution: 2.7→37.12 Å / Cor.coef. Fo:Fc: 0.8862 / Cor.coef. Fo:Fc free: 0.8865 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→37.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.92 Å / Total num. of bins used: 7
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