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Yorodumi- PDB-5ibs: Structure of E76Q, a Cancer-Associated Mutation of the Oncogenic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ibs | ||||||
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Title | Structure of E76Q, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2 | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 11 | ||||||
Keywords | HYDROLASE / TYROSINE PHOSPHATASE SHP2 / Tyrosine-protein phosphatase non-receptor type 11 | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.32 Å | ||||||
Authors | Blacklow, S.C. / Stams, T. / Fodor, M. / LaRochelle, J.R. | ||||||
Citation | Journal: Biochemistry / Year: 2016 Title: Structural and Functional Consequences of Three Cancer-Associated Mutations of the Oncogenic Phosphatase SHP2. Authors: LaRochelle, J.R. / Fodor, M. / Xu, X. / Durzynska, I. / Fan, L. / Stams, T. / Chan, H.M. / LaMarche, M.J. / Chopra, R. / Wang, P. / Fortin, P.D. / Acker, M.G. / Blacklow, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ibs.cif.gz | 401 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ibs.ent.gz | 327.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ibs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ibs_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 5ibs_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | 5ibs_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 5ibs_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/5ibs ftp://data.pdbj.org/pub/pdb/validation_reports/ib/5ibs | HTTPS FTP |
-Related structure data
Related structure data | 5i6vC 5ibmC 2shpS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60334.051 Da / Num. of mol.: 2 / Fragment: UNP residues 1-525 / Mutation: E76Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q06124, protein-tyrosine-phosphatase #2: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, 20% PEG 3350 and 1 mM TCEP |
-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: Feb 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.316→107.4 Å / Num. obs: 45260 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 44.79 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.131 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.316→2.324 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 2.1 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2SHP Resolution: 2.32→23.39 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9028 / SU R Cruickshank DPI: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.347 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.236
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Displacement parameters | Biso mean: 43.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.269 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→23.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.32→2.38 Å / Total num. of bins used: 20
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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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