+Open data
-Basic information
Entry | Database: PDB / ID: 5bk8 | |||||||||
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Title | Cancer-associated SHP2/T507K mutant | |||||||||
Components | Tyrosine-protein phosphatase non-receptor type 11 | |||||||||
Keywords | HYDROLASE / Phosphatase / SHP2 / PTPN11 / T507K | |||||||||
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 / multicellular organismal reproductive process / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / multicellular organismal reproductive process / 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 / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / negative regulation of chondrocyte differentiation / Signaling by Leptin / 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 / platelet formation / megakaryocyte development / negative regulation of type I interferon production / organ growth / triglyceride metabolic process / CTLA4 inhibitory signaling / 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 / Prolactin receptor signaling / PI-3K cascade:FGFR4 / 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 / GPVI-mediated activation cascade / cell adhesion molecule binding / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / protein dephosphorylation / Downstream signal transduction / positive regulation of mitotic cell cycle / protein-tyrosine-phosphatase / protein tyrosine kinase binding / axonogenesis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / insulin receptor binding / Spry regulation of FGF signaling / brain development / epidermal growth factor receptor signaling pathway Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Yu, Z.H. / Zhang, R.Y. / Zhang, Z.Y. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Mechanistic insights explain the transforming potential of the T507K substitution in the protein-tyrosine phosphatase SHP2. Authors: Zhang, R.Y. / Yu, Z.H. / Chen, L. / Walls, C.D. / Zhang, S. / Wu, L. / Zhang, Z.Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bk8.cif.gz | 119.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bk8.ent.gz | 89.3 KB | Display | PDB format |
PDBx/mmJSON format | 5bk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/5bk8 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/5bk8 | HTTPS FTP |
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-Related structure data
Related structure data | 4dgpS 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: 61789.719 Da / Num. of mol.: 1 / Mutation: T507K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q06124, protein-tyrosine-phosphatase |
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#2: 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: 1.99 Å3/Da / Density % sol: 38.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350, 200 mM LiCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2011 |
Diffraction measurement | Details: 1.00 degrees, 11.0 sec, detector distance 327.42 mm Method: \w scans |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.14 / Number: 105858 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 23674 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/av σ(I): 12.744 / Net I/σ(I): 12.66 / Num. measured all: 105858 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1.487 / Num. unique obs: 1139 / Rsym value: 0.811 / % possible all: 93.8 |
Cell measurement | Reflection used: 105858 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DGP Resolution: 2.25→40.658 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 25.69
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.43 Å2 / Biso mean: 31.3359 Å2 / Biso min: 10.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→40.658 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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