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Yorodumi- PDB-1ayb: CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2... -
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-Basic information
Entry | Database: PDB / ID: 1ayb | ||||||
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Title | CRYSTAL STRUCTURES OF PEPTIDE COMPLEXES OF THE AMINO-TERMINAL SH2 DOMAIN OF THE SYP TYROSINE PHOSPHATASE | ||||||
Components |
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Keywords | HYDROLASE(SH2 DOMAIN) | ||||||
Function / homology | Function and homology information IRS-mediated signalling / Signaling by ALK / IRS-related events triggered by IGF1R / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / SOS-mediated signalling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling ...IRS-mediated signalling / Signaling by ALK / IRS-related events triggered by IGF1R / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / SOS-mediated signalling / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / MET activates PTPN11 / Regulation of IFNA/IFNB signaling / Costimulation by the CD28 family / FRS-mediated FGFR1 signaling / FRS-mediated FGFR2 signaling / Tie2 Signaling / PECAM1 interactions / PI3K/AKT activation / Interleukin-20 family signaling / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / Signaling by CSF3 (G-CSF) / CTLA4 inhibitory signaling / GAB1 signalosome / PI3K Cascade / Regulation of RUNX1 Expression and Activity / Interleukin-6 signaling / negative regulation of somatostatin secretion / GPVI-mediated activation cascade / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / positive regulation of glucagon secretion / Downstream signal transduction / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / IRS activation / Interleukin-7 signaling / Spry regulation of FGF signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PD-1 signaling / Signal attenuation / epithelial cell migration / Signaling by SCF-KIT / positive regulation of signal transduction / negative regulation of hormone secretion / RAF/MAP kinase cascade / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / PIP3 activates AKT signaling / genitalia development / Platelet sensitization by LDL / atrioventricular canal development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / negative regulation of cell adhesion mediated by integrin / Interleukin-3, Interleukin-5 and GM-CSF signaling / positive regulation of fatty acid beta-oxidation / phosphatidylinositol 3-kinase activator activity / RET signaling / positive regulation of hormone secretion / cerebellar cortex formation / mammary gland development / insulin receptor complex / positive regulation of glucose metabolic process / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / transmembrane receptor protein tyrosine kinase adaptor activity / hormone metabolic process / negative regulation of chondrocyte differentiation / triglyceride metabolic process / face morphogenesis / ERBB signaling pathway / response to caffeine / positive regulation of mesenchymal cell proliferation / peptide hormone receptor binding / platelet formation / negative regulation of type I interferon production / cellular response to fatty acid / megakaryocyte development / organ growth / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / plasma membrane raft / inner ear development / phosphoprotein phosphatase activity / phospholipase binding / regulation of MAPK cascade / regulation of cell adhesion mediated by integrin / neurotrophin TRK receptor signaling pathway / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / protein localization to nucleus / non-membrane spanning protein tyrosine phosphatase activity / regulation of protein-containing complex assembly / peptidyl-tyrosine dephosphorylation / insulin receptor substrate binding / D1 dopamine receptor binding / negative regulation of insulin secretion Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Lee, C.-H. / Kuriyan, J. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Crystal structures of peptide complexes of the amino-terminal SH2 domain of the Syp tyrosine phosphatase. Authors: Lee, C.H. / Kominos, D. / Jacques, S. / Margolis, B. / Schlessinger, J. / Shoelson, S.E. / Kuriyan, J. #1: Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: Binding of a High Affinity Phosphotyrosyl Peptide to the Src Sh2 Domain: Crystal Structures of the Complexed and Peptide-Free Forms Authors: Waksman, G. / Shoelson, S.E. / Pant, N. / Cowburn, D. / Kuriyan, J. #2: Journal: Curr.Opin.Struct.Biol. / Year: 1993 Title: Structures of Sh2 and SH3 Domains Authors: Kuriyan, J. / Cowburn, D. #3: Journal: Nature / Year: 1992 Title: Crystal Structure of the Phosphotyrosine Recognition Domain Sh2 of V-Src Complexed with Tyrosine-Phosphorylated Peptides Authors: Waksman, G. / Kominos, D. / Robertson, S.R. / Pant, N. / Baltimore, D. / Birge, R.B. / Cowburn, D. / Hanafusa, H. / Mayer, B.J. / Overduin, M. / Resh, M.D. / Rios, C.B. / Silverman, L. / Kuriyan, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ayb.cif.gz | 29.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ayb.ent.gz | 21.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ayb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayb ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayb | HTTPS FTP |
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-Related 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: 11528.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P35235, protein-tyrosine-phosphatase |
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#2: Protein/peptide | Mass: 1378.335 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P35569 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.72 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å / Num. all: 5965 / Num. obs: 2549 / % possible obs: 73 % / Rmerge(I) obs: 0.089 |
-Processing
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Refinement | Resolution: 3→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.164 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3 |