+Open data
-Basic information
Entry | Database: PDB / ID: 5fbw | ||||||
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Title | PI4KB in complex with Rab11 and the MI369 Inhibitor | ||||||
Components |
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Keywords | TRANSFERASE / Inhibitor / Complex / Kinase / Lipid | ||||||
Function / homology | Function and homology information regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / rough endoplasmic reticulum membrane / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / Synthesis of PIPs at the Golgi membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / protein localization to cilium / multivesicular body assembly / phosphatidylinositol biosynthetic process / dynein light intermediate chain binding / phosphatidylinositol-mediated signaling / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of epithelial cell migration / exocytosis / inner ear development / cleavage furrow / phosphatidylinositol phosphate biosynthetic process / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / transport vesicle / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / receptor-mediated endocytosis / centriole / multivesicular body / small monomeric GTPase / G protein activity / 14-3-3 protein binding / trans-Golgi network membrane / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.487 Å | ||||||
Authors | Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E. | ||||||
Citation | Journal: To Be Published Title: PI4KB in complex with Rab11 and the MI369 Inhibitor Authors: Chalupska, D. / Mejdrova, I. / Nencka, R. / Boura, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fbw.cif.gz | 145.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fbw.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 5fbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/5fbw ftp://data.pdbj.org/pub/pdb/validation_reports/fb/5fbw | HTTPS FTP |
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-Related structure data
Related structure data | 4d0lS 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: 65264.766 Da / Num. of mol.: 1 Fragment: UNP Residues 128-422, 523-729,UNP Residues 128-422, 523-729 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB, PIK4CB / Production host: Escherichia coli (E. coli) References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase |
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#2: Protein | Mass: 24813.000 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491 |
#3: Chemical | ChemComp-5W8 / ~{ |
#4: Chemical | ChemComp-GSP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium sulfate, 0.1M MES pH=6.5, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 3.48→47.47 Å / Num. obs: 12696 / % possible obs: 98.32 % / Redundancy: 4.27 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 6.77 / Num. measured all: 54212 |
Reflection shell | Resolution: 3.48→3.61 Å / Mean I/σ(I) obs: 0.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D0L Resolution: 3.487→47.469 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.487→47.469 Å
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Refine LS restraints |
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LS refinement shell |
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