+Open data
-Basic information
Entry | Database: PDB / ID: 2shp | ||||||
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Title | TYROSINE PHOSPHATASE SHP-2 | ||||||
Components | SHP-2 | ||||||
Keywords | TYROSINE PHOSPHATASE / INSULIN SIGNALING / SH2 PROTEIN | ||||||
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 / negative regulation of chondrocyte differentiation / triglyceride metabolic process / 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 / negative regulation of type I interferon production / megakaryocyte development / organ growth / 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 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / inner ear development / phosphoprotein phosphatase activity / MAPK1 (ERK2) activation / PECAM1 interactions / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / Bergmann glial cell differentiation / regulation of type I interferon-mediated signaling pathway / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / regulation of protein-containing complex assembly / RET signaling / peptidyl-tyrosine dephosphorylation / PI3K Cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / PD-1 signaling / Regulation of IFNA/IFNB signaling / negative regulation of insulin secretion / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / homeostasis of number of cells within a tissue / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / cellular response to epidermal growth factor stimulus / FRS-mediated FGFR1 signaling / Tie2 Signaling / GPVI-mediated activation cascade / protein tyrosine kinase binding / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / cell adhesion molecule binding / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / axonogenesis / Downstream signal transduction / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein dephosphorylation / protein-tyrosine-phosphatase / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / positive regulation of glucose import / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / brain development / multicellular organism growth / insulin receptor binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT, NCS AVERAGING / Resolution: 2 Å | ||||||
Authors | Hof, P. / Pluskey, S. / Dhe-Paganon, S. / Eck, M.J. / Shoelson, S.E. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal structure of the tyrosine phosphatase SHP-2. Authors: Hof, P. / Pluskey, S. / Dhe-Paganon, S. / Eck, M.J. / Shoelson, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2shp.cif.gz | 288.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2shp.ent.gz | 234.4 KB | Display | PDB format |
PDBx/mmJSON format | 2shp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sh/2shp ftp://data.pdbj.org/pub/pdb/validation_reports/sh/2shp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.965419, -0.014739, -0.260285), Vector: |
-Components
#1: Protein | Mass: 60181.926 Da / Num. of mol.: 2 / Mutation: T2K, F41L, F513S, DEL(528-593) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q06124, protein-tyrosine-phosphatase #2: Chemical | #3: 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: 2.48 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. obs: 71634 / % possible obs: 93.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.0617 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.295 / % possible all: 82.5 |
Reflection | *PLUS Num. measured all: 276084 |
Reflection shell | *PLUS % possible obs: 82.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT, NCS AVERAGING Starting model: PTP1B AND N-TERMINAL SH2 DOMAINS Resolution: 2→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 1 Details: DATA USED AND MAPS 1SIGMA CUTOFF, R-VALUES 2SIGMA CUTOFF, 2 MOLECULES IN THE ASYMMETRIC UNIT
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Displacement parameters | Biso mean: 27.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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