Computational protocol: Structural basis for recognition of Emi2 by Polo-like kinase 1 and development of peptidomimetics blocking oocyte maturation and fertilization

Similar protocols

Protocol publication

[…] The complex Emi2169–177·Plk1-PBD (169FSQHKTSpTI177, where pT indicates phosphothreonine) was formed by mixing the phosphorylated Emi2169–177 peptide with Plk1-PBD at stoichiometry 2:1. The crystal was screened by the hanging-drop buffer diffusion method. The crystal was grown at 20 °C in 15% polyethylene glycol (PEG) 3350 and 0.1 M Tris-HCl (pH 8.5) and frozen in the buffer consisting of 30% glycerol, 15% PEG 3350, and 0.1 M Tris-HCl pH 8.5. In the case of the Emi2146–177·Plk1-PBD complex, the crystal was prepared in the buffer consisting of 10 mM MgCl2, 5 mM NiCl2,15% PEG 3350, and 0.1 M HEPES (pH 7.0) and cryoprotected by the addition of 20% of ethylene glycol. The complex of peptidomimetic 702 with Plk1-PBD was crystallized in the buffer consisting of 28% 2-propanol, 3% PEG 200, and 0.1 M Bis-Tris (pH 6.5) and frozen in 20% ethylene glycol. Datasets were recorded in Pohang Accelerator Laboratory 7A and processed by means of XDS. Molecular replacement solutions were found by means of the complex with PLHSpTA phosphopeptide in PBIP1 and Plk1-PBD1 (Protein DataBank [PDB] ID: 3P2Z) as a search model by means of Phaser. Refinement was performed in the PHENIX-Refine software, with manual rebuilding by means of COOT. Detailed data and refinement statistics are presented in . […]

Pipeline specifications

Software tools PHENIX, Coot
Application Protein structure analysis
Organisms Homo sapiens, Dipturus trachyderma