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Yorodumi- PDB-6bub: Crystal structure of the PI3KC2alpha PX domain in space group P432 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bub | ||||||
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Title | Crystal structure of the PI3KC2alpha PX domain in space group P432 | ||||||
Components | Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alpha | ||||||
Keywords | TRANSFERASE / PX domain / lipid binding / phosphoinositide / PI3-kinase | ||||||
Function / homology | Function and homology information vascular associated smooth muscle contraction / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4-phosphate 3-kinase / clathrin coat assembly / membrane organization / phosphatidylinositol biosynthetic process / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity ...vascular associated smooth muscle contraction / Synthesis of PIPs at the late endosome membrane / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol-4-phosphate 3-kinase / clathrin coat assembly / membrane organization / phosphatidylinositol biosynthetic process / phosphatidylinositol 3-kinase complex / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / phosphatidylinositol 3-kinase / clathrin-coated vesicle / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / clathrin binding / positive regulation of cell migration involved in sprouting angiogenesis / Golgi Associated Vesicle Biogenesis / exocytosis / Synthesis of PIPs at the plasma membrane / platelet-derived growth factor receptor signaling pathway / positive regulation of autophagy / phosphatidylinositol binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epidermal growth factor receptor signaling pathway / trans-Golgi network / endocytosis / insulin receptor signaling pathway / Clathrin-mediated endocytosis / vesicle / phosphorylation / intracellular membrane-bounded organelle / extracellular exosome / nucleoplasm / ATP binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.604 Å | ||||||
Authors | Chen, K.-E. / Collins, B.M. | ||||||
Citation | Journal: Structure / Year: 2018 Title: Molecular Basis for Membrane Recruitment by the PX and C2 Domains of Class II Phosphoinositide 3-Kinase-C2α. Authors: Kai-En Chen / Vikas A Tillu / Mintu Chandra / Brett M Collins / Abstract: Phosphorylation of phosphoinositides by the class II phosphatidylinositol 3-kinase (PI3K) PI3K-C2α is essential for many processes, including neuroexocytosis and formation of clathrin-coated ...Phosphorylation of phosphoinositides by the class II phosphatidylinositol 3-kinase (PI3K) PI3K-C2α is essential for many processes, including neuroexocytosis and formation of clathrin-coated vesicles. A defining feature of the class II PI3Ks is a C-terminal module composed of phox-homology (PX) and C2 membrane interacting domains; however, the mechanisms that control their specific cellular localization remain poorly understood. Here we report the crystal structure of the C2 domain of PI3K-C2α in complex with the phosphoinositide head-group mimic inositol hexaphosphate, revealing two distinct pockets for membrane binding. The C2 domain preferentially binds to phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate, and low-resolution structures of the combined PX-C2 module by small-angle X-ray scattering reveal a compact conformation in which cooperative lipid binding by each domain binding can occur. Finally, we demonstrate an unexpected role for calcium in perturbing the membrane interactions of the PX-C2 module, which we speculate may be important for regulating the activity of PI3K-C2α. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bub.cif.gz | 42.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bub.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 6bub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/6bub ftp://data.pdbj.org/pub/pdb/validation_reports/bu/6bub | HTTPS FTP |
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-Related structure data
Related structure data | 6btyC 6btzC 6bu0C 2iwlS C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 16738.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C2A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O00443, phosphatidylinositol-4-phosphate 3-kinase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.6 % / Mosaicity: 0.11 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→47.48 Å / Num. obs: 8738 / % possible obs: 99.8 % / Redundancy: 40.6 % / Biso Wilson estimate: 47.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.021 / Rrim(I) all: 0.133 / Net I/σ(I): 24.9 / Num. measured all: 354795 / Scaling rejects: 14 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 40.7 % / Rmerge(I) obs: 0.869 / Num. measured all: 41490 / Num. unique obs: 1020 / CC1/2: 0.934 / Rpim(I) all: 0.136 / Rrim(I) all: 0.88 / Net I/σ(I) obs: 4.8 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IWL Resolution: 2.604→47.483 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.74 / Stereochemistry target values: MLHL
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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: 132.91 Å2 / Biso mean: 47.7949 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.604→47.483 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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