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Yorodumi- PDB-5ih6: Human Casein Kinase 1 isoform delta (kinase domain) in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 5ih6 | ||||||
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Title | Human Casein Kinase 1 isoform delta (kinase domain) in complex with Epiblastin A derivative | ||||||
Components | Casein kinase I isoform delta | ||||||
Keywords | TRANSFERASE / Kinase domain / stem cell reprogramming / kinase inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport ...positive regulation of non-canonical Wnt signaling pathway / protein localization to Golgi apparatus / COPII vesicle coating / midbrain dopaminergic neuron differentiation / microtubule nucleation / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / protein localization to centrosome / COPII-mediated vesicle transport / tau-protein kinase activity / Golgi organization / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / endoplasmic reticulum-Golgi intermediate compartment membrane / AURKA Activation by TPX2 / ciliary basal body / cellular response to nerve growth factor stimulus / spindle microtubule / circadian regulation of gene expression / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / positive regulation of canonical Wnt signaling pathway / Circadian Clock / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / non-specific serine/threonine protein kinase / protein kinase activity / cadherin binding / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Ursu, A. / Illich, D.J. / Takemoto, Y. / Porfetye, A.T. / Zhang, M. / Brockmeyer, A. / Janning, P. / Watanabe, N. / Osada, H. / Vetter, I.R. ...Ursu, A. / Illich, D.J. / Takemoto, Y. / Porfetye, A.T. / Zhang, M. / Brockmeyer, A. / Janning, P. / Watanabe, N. / Osada, H. / Vetter, I.R. / Ziegler, S. / Schoeler, H.R. / Waldmann, H. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2016 Title: Epiblastin A Induces Reprogramming of Epiblast Stem Cells Into Embryonic Stem Cells by Inhibition of Casein Kinase 1. Authors: Ursu, A. / Illich, D.J. / Takemoto, Y. / Porfetye, A.T. / Zhang, M. / Brockmeyer, A. / Janning, P. / Watanabe, N. / Osada, H. / Vetter, I.R. / Ziegler, S. / Scholer, H.R. / Waldmann, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ih6.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ih6.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ih6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ih6_validation.pdf.gz | 832.1 KB | Display | wwPDB validaton report |
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Full document | 5ih6_full_validation.pdf.gz | 835.6 KB | Display | |
Data in XML | 5ih6_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 5ih6_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/5ih6 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/5ih6 | HTTPS FTP |
-Related structure data
Related structure data | 5ih4SC 5ih5C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34206.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal cloning artifact: GP / Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase |
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-Non-polymers , 5 types, 27 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-SRT / | ||||
#4: Chemical | #5: Chemical | ChemComp-AUG / | #6: 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: 2.79 Å3/Da / Density % sol: 55.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M Li2SO4, 0.7 - 0.8 M Na-K tartrate, 0.1 M CHES PH range: 9.3-9.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.76995 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.76995 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→37.8 Å / Num. obs: 17269 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 62.054 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.119 / Χ2: 1.126 / Net I/σ(I): 12.49 / Num. measured all: 243801 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IH4 Resolution: 2.3→37.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.952 / SU B: 15.112 / SU ML: 0.307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 218.68 Å2 / Biso mean: 89.694 Å2 / Biso min: 35.13 Å2
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Refinement step | Cycle: final / Resolution: 2.3→37.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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