Computational protocol: Structure of a Pestivirus Envelope Glycoprotein E2 Clarifies Its Role in Cell Entry

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Protocol publication

[…] Diffraction data were recorded at the Diamond Light Source I02, I03, and I24 beamlines and processed with HKL2000 (). The structure was determined with the program PHENIX AUTOSOL () by multiwavelength anomalous dispersion (MAD) phasing using selenomethionine-labeled crystals grown at neutral pH. The low pH conformation was solved by molecular replacement with MOLREP () using the neutral pH form as a search model. Manual building was performed with the program COOT () and restrained refinement (with TLS) with AUTOBUSTER (). Final models geometry were checked with MolProbity (). For data collection and refinement statistics see . [...] The superimpositions of the neutral and low pH forms were performed using SHP (). was generated with CLUSTALW () and ESPript (). The PROPKA server () was used to determine the free energy of folding of domains of BVDV1 E2 presented in . […]

Pipeline specifications

Software tools PHENIX, Molrep, Coot, MolProbity, Clustal W, ESPript, PROPKA
Application Protein structure analysis
Organisms Viruses, Bovine viral diarrhea virus 1, Sindbis virus