Computational protocol: A Novel Enterovirus 71 (EV71) Virulence Determinant: The 69th Residue of 3C Protease Modulates Pathogenicity

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Protocol publication

[…] 3C N69D were concentrated to about 10 mg/ml and rupintrivir dissolved in DMSO was added to a final concentration of 3 mM. After incubation on ice for 10 min, the mixtures were centrifuged before crystallization (Wang et al., ). The crystals were obtained in the presence of 30% PEG 8000 and 0.1 M sodium acetate (pH 4.5) after 7 days. To prevent radiation damage, crystals were equilibrated in a cryoprotectant buffer containing 15% glycerol (v/v) plus reservoir buffer and then flash frozen in a 100 K nitrogen stream. Diffraction data were collected at Shanghai Synchrotron Radiation facility (SSRF) beamline BL17 ul. The data set was processed using the HKL2000 software suite. The structure was solved by molecular replacement using PHASER with native 3C (PDB: 3SJO) as the searching model. The atomic model was built using Coot and refined using PHENIX (Adams et al., ; Emsley and Cowtan, ). Data collection and structure refinement statistics are summarized in Table . Structural figures were generated using PyMol ( […]

Pipeline specifications

Software tools Coot, PHENIX, PyMOL
Application Protein structure analysis
Organisms Homo sapiens
Diseases Hand, Foot and Mouth Disease, Nervous System Diseases, Virus Diseases