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Yorodumi- PDB-8txy: X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera -
+Open data
-Basic information
Entry | Database: PDB / ID: 8txy | ||||||
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Title | X-ray crystal structure of JRD-SIK1/2i-3 bound to a MARK2-SIK2 chimera | ||||||
Components | Serine/threonine-protein kinase MARK2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Kinase / enzyme / chimera / inhibitor | ||||||
Function / homology | Function and homology information establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / regulation of microtubule binding / mitochondrion localization / autophagy of mitochondrion / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity ...establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / regulation of microtubule binding / mitochondrion localization / autophagy of mitochondrion / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / axon development / activation of protein kinase activity / protein kinase activator activity / regulation of cytoskeleton organization / lateral plasma membrane / regulation of microtubule cytoskeleton organization / actin filament / peptidyl-threonine phosphorylation / neuron migration / tau protein binding / Wnt signaling pathway / microtubule cytoskeleton organization / positive regulation of neuron projection development / peptidyl-serine phosphorylation / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / dendrite / magnesium ion binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Raymond, D.D. / Lemke, C.T. / Shaffer, P.L. / Collins, B. / Steele, R. / Seierstad, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Identification of highly selective SIK1/2 inhibitors that modulate innate immune activation and suppress intestinal inflammation. Authors: Babbe, H. / Sundberg, T.B. / Tichenor, M. / Seierstad, M. / Bacani, G. / Berstler, J. / Chai, W. / Chang, L. / Chung, M. / Coe, K. / Collins, B. / Finley, M. / Guletsky, A. / Lemke, C.T. / ...Authors: Babbe, H. / Sundberg, T.B. / Tichenor, M. / Seierstad, M. / Bacani, G. / Berstler, J. / Chai, W. / Chang, L. / Chung, M. / Coe, K. / Collins, B. / Finley, M. / Guletsky, A. / Lemke, C.T. / Mak, P.A. / Mathur, A. / Mercado-Marin, E.V. / Metkar, S. / Raymond, D.D. / Rives, M.L. / Rizzolio, M. / Shaffer, P.L. / Smith, R. / Smith, J. / Steele, R. / Steffens, H. / Suarez, J. / Tian, G. / Majewski, N. / Volak, L.P. / Wei, J. / Desai, P.T. / Ong, L.L. / Koudriakova, T. / Goldberg, S.D. / Hirst, G. / Kaushik, V.K. / Ort, T. / Seth, N. / Graham, D.B. / Plevy, S. / Venable, J.D. / Xavier, R.J. / Towne, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8txy.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8txy.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 8txy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/8txy ftp://data.pdbj.org/pub/pdb/validation_reports/tx/8txy | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36722.520 Da / Num. of mol.: 2 Mutation: I59L, K66V V81I, L97I, V113I, M129T, S133K, G134N , S197G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MARK2, EMK1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7KZI7, non-specific serine/threonine protein kinase, tau-protein kinase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | 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: 3 Å3/Da / Density % sol: 58.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.8 / Details: 24% PEG 400, 150 mM LiSO4, 100 mM MES ph 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 48682 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 10.2 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7948 / CC1/2: 0.657 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.216 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.205 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.182
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Displacement parameters | Biso mean: 61.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.12 Å
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