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Yorodumi- PDB-4d0m: Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-G... -
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Open data
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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 informationregulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / establishment of protein localization to organelle ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / establishment of protein localization to organelle / negative regulation of adiponectin secretion / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / establishment of vesicle localization / exosomal secretion / rough endoplasmic reticulum membrane / amyloid-beta clearance by transcytosis / regulation of cilium assembly / regulation of protein transport / presynaptic endosome / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / protein transmembrane transport / Synthesis of PIPs at the Golgi membrane / regulation of vesicle-mediated transport / myosin V binding / positive regulation of cilium assembly / RAB geranylgeranylation / melanosome transport / multivesicular body assembly / phosphatidylinositol biosynthetic process / protein localization to cilium / endocytic recycling / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / dynein light intermediate chain binding / lysosome organization / mitotic metaphase chromosome alignment / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / exocytosis / inner ear development / cleavage furrow / positive regulation of epithelial cell migration / endocytic vesicle / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / intercellular bridge / transport vesicle / phagocytic vesicle / vesicle-mediated transport / 14-3-3 protein binding / multivesicular body / centriole / receptor-mediated endocytosis / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network membrane / small monomeric GTPase / regulation of cytokinesis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / small GTPase binding / centriolar satellite / Schaffer collateral - CA1 synapse / recycling endosome membrane / neuron projection development / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / endocytic vesicle membrane / synaptic vesicle membrane / G protein activity / cytoplasmic vesicle / midbody / protein-macromolecule adaptor activity / microtubule binding / molecular adaptor activity / vesicle / mitochondrial outer membrane / endosome / cilium / ciliary basal body / Golgi membrane / cell division / intracellular membrane-bounded organelle / GTPase activity / calcium ion binding / centrosome / GTP binding / protein-containing complex binding 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: 2014Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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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
| Summary document | 4d0m_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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| Full document | 4d0m_full_validation.pdf.gz | 4.7 MB | Display | |
| Data in XML | 4d0m_validation.xml.gz | 320.8 KB | Display | |
| Data in CIF | 4d0m_validation.cif.gz | 401.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/4d0m ftp://data.pdbj.org/pub/pdb/validation_reports/d0/4d0m | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4d0lSC 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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| 1 | ![]()
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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: ![]() 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: ![]() |
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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: ![]() |
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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 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting 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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HOMO SAPIENS (human)
X-RAY DIFFRACTION
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