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- PDB-4d0l: Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Ra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d0l | ||||||
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Title | Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS | ||||||
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![]() | TRANSFERASE/HYDROLASE / TRANSFERASE-HYDROLASE COMPLEX / TRANSFERASE / PHOSPHATIDYLINOSITOL 4-KINASE / PI4K / NUCLEOTIDE / GTP / RAB11 / PIK93 / SIGNALING / GTPASE / SIGNAL TRANSDUCTION / GOLGI / RECYCLING ENDOSOME / PI4P / PHOSPHOINOSITIDE / PTDINS4P / PI4KB | ||||||
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. / Inglis, A.J. / Perisic, O. / Masson, G.R. / McLaughin, S.H. / Rutaganira, F. / Shokat, K.M. / Williams, R.L. | ||||||
![]() | ![]() Title: Structures of Pi4Kiiibeta Complexes Show Simultaneous Recruitment of Rab11 and its Effectors. Authors: Burke, J.E. / Inglis, A.J. / Perisic, O. / Masson, G.R. / Mclaughlin, S.H. / Rutaganira, F. / Shokat, K.M. / Williams, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 409.2 KB | Display | ![]() |
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PDB format | ![]() | 328.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 71.7 KB | Display | |
Data in CIF | ![]() | 95.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d0mC ![]() 1oiwS ![]() 3ihyS C: citing same article ( S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _
NCS ensembles :
NCS oper:
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Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 64593.141 Da / Num. of mol.: 3 / Fragment: RESIDUES 121-407,508-784 / Mutation: YES Source method: isolated from a genetically manipulated source Details: HDX-OPTIMISED DELETION VARIANT / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase #2: Protein | Mass: 24691.818 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 27 molecules ![](data/chem/img/093.gif)
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THREE HDX-OPTIMIZED DELETIONS AND S294A MUTATION. ISOFORM 2 OF UNIPROT Q9UBF8 (CHAINS ACE) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 5.6 Details: 15% (W/V) PEG 4000, 0.1 M NA CITRATE PH 5.6, AND 0.2 M AMMONIUM ACETATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 18, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.51 Å / Num. obs: 70875 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.8→2.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3IHY AND 1OIW Resolution: 2.94→115.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 22.398 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.221 Å2
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Refinement step | Cycle: LAST / Resolution: 2.94→115.84 Å
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Refine LS restraints |
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