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Yorodumi- PDB-7fic: Reversible lysine-targeted probes reveal residence time-based kin... -
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-Basic information
Entry | Database: PDB / ID: 7fic | ||||||
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Title | Reversible lysine-targeted probes reveal residence time-based kinase selectivity in vivo | ||||||
Components | Aurora kinase A | ||||||
Keywords | CELL CYCLE / Reversible lysine-targeted inhibitors / kinase | ||||||
Function / homology | Function and homology information Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / positive regulation of oocyte maturation / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / regulation of G2/M transition of mitotic cell cycle / SUMOylation of DNA replication proteins / spindle midzone / centriole / protein serine/threonine/tyrosine kinase activity / liver regeneration / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / molecular function activator activity / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / mitotic spindle / kinetochore / G2/M transition of mitotic cell cycle / response to wounding / spindle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / basolateral plasma membrane / midbody / Regulation of TP53 Activity through Phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein autophosphorylation / microtubule / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / negative regulation of apoptotic process / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Craven, G.B. / Wan, X.B. / Taunton, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2022 Title: Reversible lysine-targeted probes reveal residence time-based kinase selectivity. Authors: Yang, T. / Cuesta, A. / Wan, X. / Craven, G.B. / Hirakawa, B. / Khamphavong, P. / May, J.R. / Kath, J.C. / Lapek Jr., J.D. / Niessen, S. / Burlingame, A.L. / Carelli, J.D. / Taunton, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fic.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fic.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 7fic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/7fic ftp://data.pdbj.org/pub/pdb/validation_reports/fi/7fic | HTTPS FTP |
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-Related structure data
Related structure data | 4cegS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30718.256 Da / Num. of mol.: 1 / Mutation: C290A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O14965, non-specific serine/threonine protein kinase | ||||
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#2: Chemical | ChemComp-5YZ / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M lithium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11685 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11685 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→76.21 Å / Num. obs: 15223 / % possible obs: 99.9 % / Redundancy: 19.5 % / Biso Wilson estimate: 85.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.011 / Rrim(I) all: 0.05 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 2.32→2.403 Å / Rmerge(I) obs: 2.109 / Num. unique obs: 1516 / CC1/2: 0.642 / Rrim(I) all: 2.163 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CEG Resolution: 2.32→76.17 Å / SU ML: 0.4137 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.6528 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 90.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→76.17 Å
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Refine LS restraints |
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LS refinement shell |
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