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Yorodumi- PDB-5df6: Crystal structure of PTPN11 tandem SH2 domains in complex with a ... -
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-Basic information
Entry | Database: PDB / ID: 5df6 | |||||||||
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Title | Crystal structure of PTPN11 tandem SH2 domains in complex with a TXNIP peptide | |||||||||
Components |
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Keywords | HYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC | |||||||||
Function / homology | Function and homology information cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / negative regulation of cell division / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin ...cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / negative regulation of cell division / 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 / enzyme inhibitor activity / face morphogenesis / ERBB signaling pathway / Regulation of FOXO transcriptional activity by acetylation / 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 / 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 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / MAPK1 (ERK2) activation / PECAM1 interactions / phosphoprotein phosphatase activity / Bergmann glial cell differentiation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / neurotrophin TRK receptor signaling pathway / inner ear development / platelet-derived growth factor receptor signaling pathway / The NLRP3 inflammasome / non-membrane spanning protein tyrosine phosphatase activity / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / Regulation of IFNA/IFNB signaling / PD-1 signaling / negative regulation of insulin secretion / 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 / response to glucose / Purinergic signaling in leishmaniasis infection / Regulation of IFNG signaling / response to mechanical stimulus / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / keratinocyte differentiation / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / GPVI-mediated activation cascade / cell adhesion molecule binding / cellular response to epidermal growth factor stimulus / Tie2 Signaling / 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 / axonogenesis / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein tyrosine kinase binding / protein-tyrosine-phosphatase / DNA damage checkpoint signaling / protein tyrosine phosphatase activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.78 Å | |||||||||
Authors | Dong, A. / Li, W. / Tempel, W. / Liu, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: Biochem.J. / Year: 2016 Title: Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP. Authors: Liu, Y. / Lau, J. / Li, W. / Tempel, W. / Li, L. / Dong, A. / Narula, A. / Qin, S. / Min, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5df6.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5df6.ent.gz | 44.6 KB | Display | PDB format |
PDBx/mmJSON format | 5df6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/5df6 ftp://data.pdbj.org/pub/pdb/validation_reports/df/5df6 | HTTPS FTP |
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-Related structure data
Related structure data | 5cq2C 3tkzS 4xz0S S: Starting model for refinement C: citing same article (ref.) |
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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: 28750.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Plasmid: pET28-SacB-AP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q06124, protein-tyrosine-phosphatase | ||||
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#2: Protein/peptide | Mass: 1503.610 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3M7*PLUS #3: Chemical | ChemComp-UNX / #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: 1.98 Å3/Da / Density % sol: 37.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / Details: 20% PEG-3350, 0.2 M ammonium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→46.69 Å / Num. obs: 23333 / % possible obs: 98.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.78→1.82 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.4 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Starting model: 3TKZ AND 4XZ0 Resolution: 1.78→46.69 Å / SU B: 3.725 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.133 Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. PHENIX.MOLPROBITY WAS USED FOR GEOMETRY VALIDATION. JLIGAND AND THE GRADE SERVER WERE USED IN RESTRAINT PREPARATION.
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Displacement parameters | Biso mean: 30.51 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→46.69 Å
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