Computational protocol: Structural characterisation of human galectin-4 N-terminal carbohydrate recognition domain in complex with glycerol, lactose, 3′-sulfo-lactose, and 2′-fucosyllactose

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Protocol publication

[…] All X-ray data collection experiments were conducted at the Australian Synchrotron MX1 and MX2 beamlines. Galectin-4N crystals were dipped in cryo-protectant solutions (30% w/v PEG 3350, 0.2 M CaCl2, 7% v/v glycerol for galectin-4N-Lactose complex and 4.0 M sodium formate, 0.1 M Tris pH 8.0, 10% v/v glycerol for others) before being flash-cooled in liquid nitrogen. The X-ray diffraction data were indexed and integrated using XDS or iMOSFLM and scaled and merged using Aimless as implemented in the CCP4 suite of crystallographic software. Galectin-4N protein sequence (aa. 1–155) was used to build a molecular replacement model via the SWISS-MODEL server with mouse galectin-4N structure (PDB ID: 3I8T) as template. The structures were solved by molecular replacement using the homology model with Phaser and were refined using Refmac5. Visualization of electron density and model-building was performed using Coot and the models were validated and analysed by Molprobity. […]

Pipeline specifications

Software tools XDS, iMosflm, CCP4, SWISS-MODEL, REFMAC5, Coot, MolProbity
Applications Small-angle scattering, Protein structure analysis
Organisms Homo sapiens, Dipturus trachyderma
Diseases Neoplasms
Chemicals Fucose, Glycerol, Hydrogen, Lactose, Oxygen