[English] 日本語

- PDB-5lhz: PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5lhz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL | |||||||||
![]() |
| |||||||||
![]() | STRUCTURAL PROTEIN / Polo box domain / Centriole / Complex / transferase | |||||||||
Function / homology | ![]() floor plate development / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / embryonic axis specification / trophoblast giant cell differentiation / notochord development ...floor plate development / de novo centriole assembly involved in multi-ciliated epithelial cell differentiation / procentriole / deuterosome / regulation of centriole replication / procentriole replication complex / positive regulation of centriole replication / embryonic axis specification / trophoblast giant cell differentiation / notochord development / microtubule organizing center organization / polo kinase / positive regulation of spindle assembly / XY body / protein localization to centrosome / determination of left/right symmetry / neural tube development / smoothened signaling pathway / heart looping / forebrain development / microtubule organizing center / centriole replication / cleavage furrow / centrosome duplication / cilium assembly / positive regulation of G1/S transition of mitotic cell cycle / centriole / 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 / regulation of mitotic spindle organization / AURKA Activation by TPX2 / mitotic spindle organization / neural tube closure / multicellular organism growth / Regulation of PLK1 Activity at G2/M Transition / cell cortex / in utero embryonic development / protein phosphorylation / ciliary basal body / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / negative regulation of apoptotic process / nucleolus / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Cottee, M.A. / Lea, S.M. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: A key centriole assembly interaction interface between human PLK4 and STIL appears to not be conserved in flies. Authors: Cottee, M.A. / Johnson, S. / Raff, J.W. / Lea, S.M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 121.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 466.4 KB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lhwC ![]() 5lhxC ![]() 5lhyC ![]() 4yypS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 9915.191 Da / Num. of mol.: 3 / Fragment: UNP residues 884-970 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 3199.662 Da / Num. of mol.: 3 / Fragment: UNP residues 726-750 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % / Description: Hexagonal rod |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→36.223 Å / Num. obs: 13265 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.995 / Net I/σ(I): 12.1 |
Reflection shell | Highest resolution: 2.51 Å / Rmerge(I) obs: 1.312 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Model based on 4YYP Resolution: 2.51→36.223 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.21
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→36.223 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|