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Yorodumi- PDB-6ru7: Crystal structure of Casein Kinase I delta (CK1d) in complex with... -
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-Basic information
Entry | Database: PDB / ID: 6ru7 | ||||||
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Title | Crystal structure of Casein Kinase I delta (CK1d) in complex with double phosphorylated p63 PAD2P peptide | ||||||
Components |
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Keywords | TRANSFERASE / CK1 delta / CK1delta / CSNK1D / TP63 / p63 / kinase substrate complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / positive regulation of non-canonical Wnt signaling pathway / establishment of planar polarity / positive regulation of keratinocyte proliferation ...ectoderm and mesoderm interaction / epidermal cell division / cloacal septation / positive regulation of somatic stem cell population maintenance / prostatic bud formation / negative regulation of mesoderm development / female genitalia morphogenesis / positive regulation of non-canonical Wnt signaling pathway / establishment of planar polarity / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / polarized epithelial cell differentiation / negative regulation of intracellular estrogen receptor signaling pathway / proximal/distal pattern formation / protein localization to Golgi apparatus / positive regulation of fibroblast apoptotic process / positive regulation of cell cycle G1/S phase transition / WW domain binding / skin morphogenesis / cranial skeletal system development / midbrain dopaminergic neuron differentiation / COPII vesicle coating / sympathetic nervous system development / microtubule nucleation / post-anal tail morphogenesis / tau-protein kinase / non-motile cilium assembly / protein localization to cilium / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / protein localization to centrosome / COPII-mediated vesicle transport / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / hair follicle morphogenesis / tau-protein kinase activity / positive regulation of Notch signaling pathway / regulation of epidermal cell division / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of stem cell proliferation / epithelial cell development / TP53 Regulates Transcription of Caspase Activators and Caspases / Golgi organization / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / keratinocyte proliferation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / establishment of skin barrier / Pyroptosis / positive regulation of osteoblast differentiation / keratinocyte differentiation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / MDM2/MDM4 family protein binding / Notch signaling pathway / 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 / cellular response to nerve growth factor stimulus / ciliary basal body / stem cell proliferation / skeletal system development / determination of adult lifespan / promoter-specific chromatin binding / TP53 Regulates Metabolic Genes / positive regulation of apoptotic signaling pathway / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / spindle microtubule / regulation of circadian rhythm / Wnt signaling pathway / spindle / endocytosis / Regulation of PLK1 Activity at G2/M Transition / cellular senescence / Circadian Clock / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / transcription by RNA polymerase II / damaged DNA binding / non-specific serine/threonine protein kinase / DNA-binding transcription factor activity, RNA polymerase II-specific / protein kinase activity / chromatin remodeling / cadherin binding / positive regulation of protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Chaikuad, A. / Tuppi, M. / Gebel, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Dotsch, V. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Authors: Gebel, J. / Tuppi, M. / Chaikuad, A. / Hotte, K. / Schroder, M. / Schulz, L. / Lohr, F. / Gutfreund, N. / Finke, F. / Henrich, E. / Mezhyrova, J. / Lehnert, R. / Pampaloni, F. / Hummer, G. / ...Authors: Gebel, J. / Tuppi, M. / Chaikuad, A. / Hotte, K. / Schroder, M. / Schulz, L. / Lohr, F. / Gutfreund, N. / Finke, F. / Henrich, E. / Mezhyrova, J. / Lehnert, R. / Pampaloni, F. / Hummer, G. / Stelzer, E.H.K. / Knapp, S. / Dotsch, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ru7.cif.gz | 265.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ru7.ent.gz | 213.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ru7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ru7_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6ru7_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6ru7_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 6ru7_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/6ru7 ftp://data.pdbj.org/pub/pdb/validation_reports/ru/6ru7 | HTTPS FTP |
-Related structure data
Related structure data | 6ru6C 6ru8C 4hnfS 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 34424.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CSNK1D, HCKID / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2 References: UniProt: P48730, non-specific serine/threonine protein kinase, tau-protein kinase #2: Protein/peptide | Mass: 1719.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3D4 |
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-Non-polymers , 4 types, 244 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-NA / | #6: 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: 2.38 Å3/Da / Density % sol: 48.37 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 10-20% PEG 3350, 0.1-0.2 M sodium sulfate and 0.1 M citrate, pH 4.6-5.9 PH range: 4.6-5.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.08→46.6 Å / Num. obs: 41053 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.05 / Rrim(I) all: 0.125 / Net I/σ(I): 8.6 / Num. measured all: 248293 / Scaling rejects: 27 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HNF Resolution: 2.08→46.6 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 10.187 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.171 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 143.55 Å2 / Biso mean: 44.001 Å2 / Biso min: 25.45 Å2
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Refinement step | Cycle: final / Resolution: 2.08→46.6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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