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- PDB-5c46: Crystal structure of an engineered construct of phosphatidylinosi... -
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Basic information
Entry | Database: PDB / ID: 5c46 | ||||||
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Title | Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta in complex with GTP gamma S loaded Rab11 | ||||||
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![]() | Transferase/Signaling Protein / Protein-protein complex / lipid kinase / GTPase complex / Transferase-Signaling Protein complex | ||||||
Function / homology | ![]() 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 / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / 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 / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / melanosome transport / rough endoplasmic reticulum membrane / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / VxPx cargo-targeting to cilium / Synthesis of PIPs at the Golgi membrane / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / multivesicular body assembly / phosphatidylinositol biosynthetic process / protein localization to cilium / dynein light intermediate chain binding / 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 / phosphatidylinositol-mediated signaling / cleavage furrow / phosphatidylinositol phosphate biosynthetic process / inner ear development / centriolar satellite / mitotic spindle assembly / vesicle-mediated transport / transport vesicle / 14-3-3 protein binding / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / phagocytic vesicle / multivesicular body / small monomeric GTPase / receptor-mediated endocytosis / G protein activity / trans-Golgi network membrane / regulation of cytokinesis / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Burke, J.E. / Fowler, M.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIII beta with Rab11. Authors: Fowler, M.L. / McPhail, J.A. / Jenkins, M.L. / Masson, G.R. / Rutaganira, F.U. / Shokat, K.M. / Williams, R.L. / Burke, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 282.2 KB | Display | ![]() |
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PDB format | ![]() | 225.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755 KB | Display | ![]() |
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Full document | ![]() | 759.8 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5c4gC ![]() 4d0lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules EF
#1: Protein | Mass: 60683.840 Da / Num. of mol.: 1 / Mutation: S294A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase |
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#2: Protein | Mass: 24691.818 Da / Num. of mol.: 1 / Mutation: Q70L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 8 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GSP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GSP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-GSP / | #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.99 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG-4000, sodium citrate, ammonium sulfate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 12, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.65→48.98 Å / Num. obs: 27529 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 61.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.047 / Net I/σ(I): 12.2 / Num. measured all: 173010 / Scaling rejects: 1209 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D0L Resolution: 2.65→48.975 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.87 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 154.59 Å2 / Biso mean: 82.1371 Å2 / Biso min: 38.95 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.65→48.975 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: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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