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Yorodumi- PDB-9b3s: Crystal structure of casein kinase 1 delta 1 with tethered phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9b3s | ||||||
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Title | Crystal structure of casein kinase 1 delta 1 with tethered phosphorylated tail | ||||||
Components | Casein kinase I isoform delta | ||||||
Keywords | TRANSFERASE / CIRCADIAN CLOCK PROTEIN / kinase / serine-threonine kinase | ||||||
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 / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / 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 / Resolution: 2.4 Å | ||||||
Authors | Harold, R.L. / Yaitanes, N. / Tripathi, S.T. / Partch, C.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Isoform-specific C-terminal phosphorylation drives autoinhibition of Casein Kinase 1. Authors: Harold, R.L. / Tulsian, N.K. / Narasimamurthy, R. / Yaitanes, N. / Ayala Hernandez, M.G. / Lee, H. / Tripathi, S.M. / Crosby, P. / Virshup, D.M. / Partch, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9b3s.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9b3s.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 9b3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9b3s_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 9b3s_full_validation.pdf.gz | 455.1 KB | Display | |
Data in XML | 9b3s_validation.xml.gz | 29 KB | Display | |
Data in CIF | 9b3s_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/9b3s ftp://data.pdbj.org/pub/pdb/validation_reports/b3/9b3s | HTTPS FTP |
-Related structure data
Related structure data | 6pxoS 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
#1: Protein | Mass: 37057.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-294, 390-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Production host: Escherichia coli (E. coli) References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase #2: 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: 2.47 Å3/Da / Density % sol: 50.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% PEG3350, 0.2 M succinic acid, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.933 Å / Num. obs: 25723 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.175 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 2 / Num. unique obs: 2688 / CC1/2: 0.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6PXO Resolution: 2.4→45.933 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.56 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→45.933 Å
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Refine LS restraints |
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LS refinement shell |
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