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Yorodumi- PDB-5tq1: Phospholipase C gamma-1 C-terminal SH2 domain bound to a phosphop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tq1 | ||||||
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Title | Phospholipase C gamma-1 C-terminal SH2 domain bound to a phosphopeptide derived from the insulin receptor | ||||||
Components |
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Keywords | HYDROLASE / SH2 / Phospholipase / phosphopeptide | ||||||
Function / homology | Function and homology information response to vanadate(3-) / Insulin receptor signalling cascade / Signaling by Insulin receptor / IRS activation / calcium-dependent phospholipase C activity / yolk / : / Insulin receptor recycling / embryonic liver development / 3-phosphoinositide-dependent protein kinase binding ...response to vanadate(3-) / Insulin receptor signalling cascade / Signaling by Insulin receptor / IRS activation / calcium-dependent phospholipase C activity / yolk / : / Insulin receptor recycling / embryonic liver development / 3-phosphoinositide-dependent protein kinase binding / Signal attenuation / phosphoinositide phospholipase C / positive regulation of glycoprotein biosynthetic process / lipoic acid binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / response to resveratrol / phospholipid catabolic process / regulation of hydrogen peroxide metabolic process / alternative mRNA splicing, via spliceosome / phosphatidylinositol metabolic process / negative regulation of glycogen biosynthetic process / regulation of female gonad development / positive regulation of meiotic cell cycle / cellular response to zinc ion starvation / positive regulation of developmental growth / insulin-like growth factor II binding / phosphatidylinositol phospholipase C activity / male sex determination / exocrine pancreas development / COP9 signalosome / response to vitamin D / insulin receptor complex / insulin-like growth factor I binding / insulin receptor activity / negative regulation of transporter activity / phosphatidylinositol-mediated signaling / positive regulation of kinase activity / positive regulation of protein-containing complex disassembly / cargo receptor activity / response to manganese ion / response to food / dendritic spine maintenance / insulin binding / PTB domain binding / neuronal cell body membrane / regulation of gluconeogenesis / adrenal gland development / response to testosterone / positive regulation of epithelial cell migration / response to starvation / protein tyrosine kinase activator activity / negative regulation of feeding behavior / fat cell differentiation / amyloid-beta clearance / activation of protein kinase activity / positive regulation of respiratory burst / regulation of embryonic development / positive regulation of receptor internalization / insulin receptor substrate binding / epidermis development / positive regulation of glycogen biosynthetic process / cellular response to vascular endothelial growth factor stimulus / response to tumor necrosis factor / response to glucose / phosphatidylinositol 3-kinase binding / heart morphogenesis / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / positive regulation of phosphorylation / response to glucocorticoid / cellular response to epidermal growth factor stimulus / ruffle / dendrite membrane / insulin-like growth factor receptor binding / receptor-mediated endocytosis / neuron projection maintenance / activation of protein kinase B activity / cerebellum development / positive regulation of glycolytic process / response to hormone / response to nutrient levels / guanyl-nucleotide exchange factor activity / positive regulation of mitotic nuclear division / negative regulation of protein phosphorylation / liver development / response to activity / response to organic substance / molecular function activator activity / liver regeneration / caveola / hippocampus development / positive regulation of glucose import / animal organ morphogenesis / response to insulin / positive regulation of MAP kinase activity / epidermal growth factor receptor signaling pathway / receptor internalization / receptor protein-tyrosine kinase / cellular response to growth factor stimulus / peptidyl-tyrosine phosphorylation Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.485 Å | ||||||
Authors | Wuttke, D.S. / McKercher, M.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Multimodal Recognition of Diverse Peptides by the C-Terminal SH2 Domain of Phospholipase C-gamma 1 Protein. Authors: McKercher, M.A. / Guan, X. / Tan, Z. / Wuttke, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tq1.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tq1.ent.gz | 44.8 KB | Display | PDB format |
PDBx/mmJSON format | 5tq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/5tq1 ftp://data.pdbj.org/pub/pdb/validation_reports/tq/5tq1 | HTTPS FTP |
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-Related structure data
Related structure data | 5tnwC 5to4C 5tqsC 4k44S 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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Unit cell |
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-Components
#1: Protein | Mass: 11989.685 Da / Num. of mol.: 1 / Fragment: UNP residues 663-759 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: PLCG1 / Plasmid: pET15b / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) References: UniProt: P08487, phosphoinositide phospholipase C |
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#2: Protein/peptide | Mass: 1387.340 Da / Num. of mol.: 1 / Fragment: UNP residues 9-19 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q9R1H1, UniProt: P15127*PLUS |
#3: 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: 2.12 Å3/Da / Density % sol: 42.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1M Tris (pH 9.0), 30% PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.485→58.665 Å / Num. all: 18758 / Num. obs: 18758 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 15.76 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/av σ(I): 7.218 / Net I/σ(I): 16.5 / Num. measured all: 104032 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K44 Resolution: 1.485→29.332 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.24 Å2 / Biso mean: 21.0886 Å2 / Biso min: 6.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.485→29.332 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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