[English] 日本語
Yorodumi- PDB-6n45: Crystal structure of the cryptic polo box domain of human activat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n45 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the cryptic polo box domain of human activated Plk4 variant 1 | ||||||
Components | Chimera protein of Serine/threonine-protein kinase PLK4 and DDB1- and CUL4-associated factor 1 | ||||||
Keywords | CELL CYCLE / Polo-like kinase 4 / protein phosphorylation / centriole duplication / PCM organization / phase separation | ||||||
Function / homology | Function and homology information de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / histone H2AT120 kinase activity / procentriole replication complex / cell competition in a multicellular organism / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / V(D)J recombination ...de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / histone H2AT120 kinase activity / procentriole replication complex / cell competition in a multicellular organism / positive regulation of centriole replication / trophoblast giant cell differentiation / polo kinase / V(D)J recombination / XY body / Cul4-RING E3 ubiquitin ligase complex / centriole replication / cleavage furrow / ubiquitin-like ligase-substrate adaptor activity / cilium 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 / centriole / AURKA Activation by TPX2 / B cell differentiation / post-translational protein modification / mitotic spindle organization / nuclear estrogen receptor binding / kinetochore / fibrillar center / spindle pole / positive regulation of protein catabolic process / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / non-specific serine/threonine protein kinase / protein ubiquitination / phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Zhang, L. / Park, J.-E. / Meng, L. / Lee, K.S. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Phase separation of Polo-like kinase 4 by autoactivation and clustering drives centriole biogenesis. Authors: Park, J.E. / Zhang, L. / Bang, J.K. / Andresson, T. / DiMaio, F. / Lee, K.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6n45.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6n45.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 6n45.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n45_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6n45_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 6n45_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6n45_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/6n45 ftp://data.pdbj.org/pub/pdb/validation_reports/n4/6n45 | HTTPS FTP |
-Related structure data
Related structure data | 6n46C 4n9jS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30590.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLK4, SAK, STK18, DCAF1, KIAA0800, RIP, VPRBP / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: O00444, UniProt: Q9Y4B6, polo kinase, non-specific serine/threonine protein kinase |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.05 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4.3M Ammonium Acetate 0.1M BisTris propane pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. obs: 17096 / % possible obs: 99.9 % / Redundancy: 11.7 % / Net I/σ(I): 49.7 |
Reflection shell | Resolution: 2.64→2.73 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 2.8 / CC1/2: 0.886 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N9J Resolution: 2.64→34.77 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.873 / SU B: 27.42 / SU ML: 0.262 / Cross valid method: FREE R-VALUE / ESU R: 0.509 / ESU R Free: 0.359 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.374 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.64→34.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|