+Open data
-Basic information
Entry | Database: PDB / ID: 7n80 | ||||||
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Title | Crystal Structure of PI5P4KIIBeta | ||||||
Components | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta | ||||||
Keywords | TRANSFERASE / Kinase | ||||||
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: 2.5 Å | ||||||
Authors | Chen, S. / Ha, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Pharmacological inhibition of PI5P4K alpha / beta disrupts cell energy metabolism and selectively kills p53-null tumor cells. Authors: Chen, S. / Chandra Tjin, C. / Gao, X. / Xue, Y. / Jiao, H. / Zhang, R. / Wu, M. / He, Z. / Ellman, J. / Ha, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n80.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n80.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 7n80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n80 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n80 | HTTPS FTP |
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-Related structure data
Related structure data | 7n6zC 7n71C 7n7jC 7n7kC 7n7lC 7n7mC 7n7nC 7n7oC 7n81C 1bo1S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44800.773 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: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.78 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.15 M DL-Malic acid pH 7.0, 20% (w/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→40 Å / Num. obs: 24659 / % possible obs: 89 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.093 / Rrim(I) all: 0.16 / Χ2: 1.098 / Net I/σ(I): 4.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BO1 Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.704 / SU ML: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 155.53 Å2 / Biso mean: 60.981 Å2 / Biso min: 28.7 Å2
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Refinement step | Cycle: final / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.531 Å / Rfactor Rfree error: 0
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