Crystal structure of Saccharomyces cerevisiae Vps15 WD repeat domain
Components
Serine/threonine-protein kinase VPS15
Keywords
SIGNALING PROTEIN / PROTEIN BINDING / seven-bladed propeller / WD repeat / scaffold protein / ATP-binding / Endosome / Golgi apparatus / Kinase / Lipoprotein / Membrane / Myristate / Nucleotide-binding / Phosphoprotein / Protein transport / Serine/threonine-protein kinase / Transferase / Transport
Function / homology
Function and homology information
Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / Synthesis of PIPs at the Golgi membrane / vacuole-isolation membrane contact site / vacuole inheritance / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / Macroautophagy ...Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the late endosome membrane / RHO GTPases Activate NADPH Oxidases / nucleus-vacuole junction / Synthesis of PIPs at the Golgi membrane / vacuole-isolation membrane contact site / vacuole inheritance / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / Macroautophagy / protein retention in Golgi apparatus / pexophagy / phagophore assembly site membrane / protein targeting to vacuole / late endosome to vacuole transport / fungal-type vacuole membrane / phosphatidylinositol phosphate biosynthetic process / ubiquitin binding / macroautophagy / positive regulation of transcription elongation by RNA polymerase II / autophagy / late endosome / endosome membrane / non-specific serine/threonine protein kinase / phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding Similarity search - Function
Serine/threonine-protein kinase Vps15-like / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site ...Serine/threonine-protein kinase Vps15-like / HEAT repeat profile. / HEAT, type 2 / Armadillo-like helical / Armadillo-type fold / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal grow
Temperature: 291 K / Method: macroseeding into microbatch / pH: 6.5 Details: 0.7 M ammonium malonate, 0.05 M sodium acetate, 2% 2-propanol, pH 6.5, macroseeding into microbatch, temperature 291K
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2007
Radiation
Monochromator: Double crystal monochromator, Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Redundancy: 21.5 % / Av σ(I) over netI: 36 / Number: 637020 / Rmerge(I) obs: 0.097 / Χ2: 1.03 / D res high: 2.2 Å / D res low: 30 Å / Num. obs: 29652 / % possible obs: 100
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