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Yorodumi- PDB-4d0m: Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d0m | ||||||
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Title | Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-GTP- gamma-S and the Rab-binding domain of FIP3 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / PHOSPHOINOSITIDE / PHOSPHATIDYLINOSITOL 4-KINASE / LIPID KINASE / FAMILY OF RAB INTERACTING PROTEINS / FIP3 / RAB-BINDING DOMAIN / RBD / RAB11 / GTP / PIK93 / GOLGI / RECYCLING ENDOSOME | ||||||
Function / homology | Function and homology information postsynaptic recycling endosome membrane / 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 ...postsynaptic recycling endosome membrane / 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 / negative regulation of adiponectin secretion / 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 / endocytic recycling / 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 / intercellular bridge / positive regulation of epithelial cell migration / exocytosis / inner ear development / phosphatidylinositol-mediated signaling / cleavage furrow / phosphatidylinositol phosphate biosynthetic process / mitotic spindle assembly / endocytic vesicle / centriolar satellite / phagocytic vesicle / transport vesicle / vesicle-mediated transport / positive regulation of G2/M transition of mitotic cell cycle / Anchoring of the basal body to the plasma membrane / receptor-mediated endocytosis / centriole / multivesicular body / small monomeric GTPase / G protein activity / trans-Golgi network membrane / 14-3-3 protein binding / 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 / small GTPase binding / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / midbody / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / molecular adaptor activity / endosome / cell cycle / cell division / phosphorylation / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / calcium ion binding / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å | ||||||
Authors | Burke, J.E. / Inglis, A.J. / Perisic, O. / Masson, G.R. / McLaughlin, S.H. / Rutaganira, F. / Shokat, K.M. / Williams, R.L. | ||||||
Citation | Journal: Science / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d0m.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4d0m.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 4d0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d0m ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d0m | HTTPS FTP |
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-Related structure data
Related structure data | 4d0lSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 24 molecules ACGIMOQSWYcgBDHJNPRTXZdh
#1: Protein | Mass: 64593.141 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Details: HDX-OPTIMIZED DELETION VARIANT / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACEBAC1-HSPI4KIIIB/PJB143 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase #2: Protein | Mass: 24691.818 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPTG/PJB88 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P62491, small monomeric GTPase |
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-Protein/peptide , 1 types, 12 molecules EFKLUVabefij
#3: Protein/peptide | Mass: 5584.360 Da / Num. of mol.: 12 / Fragment: RAB-BINDING DOMAIN / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PJB164-POPTG-HSFIP3 (713-756) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O75154 |
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-Non-polymers , 3 types, 36 molecules
#4: Chemical | ChemComp-093 / #5: Chemical | ChemComp-GSP / #6: Chemical | ChemComp-MG / |
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-Details
Sequence details | THREE HDX-OPTIMISED DELETIONS AND S294A MUTATION |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE |
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Crystal grow | Details: 16% PEG 6K, 0.01 M NA CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.968629 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968629 Å / Relative weight: 1 |
Reflection | Resolution: 6→49.88 Å / Num. obs: 37822 / % possible obs: 95.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 6→6.27 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.2 / % possible all: 97 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D0L Resolution: 6→294.32 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.789 / SU B: 262.603 / SU ML: 2.522 / Cross valid method: THROUGHOUT / ESU R Free: 3.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES REFINED INDIVIDUALLY BECAUSE OF THE LOW RESOLUTION, WE MADE NO MANUAL READJUSTMENTS OF THE MODEL FOLLOWING RESTRAINED REFINEMENT WITH REFMAC.
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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: 261.052 Å2
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Refinement step | Cycle: LAST / Resolution: 6→294.32 Å
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Refine LS restraints |
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