+Open data
-Basic information
Entry | Database: PDB / ID: 7em1 | ||||||
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Title | Crystal structure of the PI5P4Kbeta-ITP complex | ||||||
Components | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | ||||||
Keywords | TRANSFERASE / Lipid Kinase / Phosphoinositide signaling | ||||||
Function / homology | Function and homology information 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome / negative regulation of insulin receptor signaling pathway / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / phosphorylation / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Senda, M. / Senda, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Structure / Year: 2022 Title: The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity. Authors: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / ...Authors: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / Sasaki, A.T. / Senda, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7em1.cif.gz | 260.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7em1.ent.gz | 207.3 KB | Display | PDB format |
PDBx/mmJSON format | 7em1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/7em1 ftp://data.pdbj.org/pub/pdb/validation_reports/em/7em1 | HTTPS FTP |
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-Related structure data
Related structure data | 6k4gC 6k4hC 7em2C 7em3C 7em4C 7em5C 7em6C 7em7C 7em8C 3x04S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44928.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2B, PIP5K2B / Production host: Escherichia coli (E. coli) References: UniProt: P78356, 1-phosphatidylinositol-5-phosphate 4-kinase #2: Chemical | #3: Chemical | ChemComp-CZU / [[( | Has ligand of interest | Y | |
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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: 2.97 Å3/Da / Density % sol: 58.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 22, 2018 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→69.69 Å / Num. obs: 31457 / % possible obs: 99.9 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.57 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.845 / Num. unique obs: 4447 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3X04 Resolution: 2.65→45.653 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→45.653 Å
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Refine LS restraints |
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LS refinement shell |
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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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