Computational protocol: Molecular basis for defect in Alix-binding by alternatively spliced isoform of ALG-2 (ALG-2ΔGF122) and structural roles of F122 in target recognition

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Protocol publication

[…] X-ray diffraction data were collected at beamlines BL-5A and NW-12 of Photon Factory (Tsukuba, Japan) under cryogenic conditions with crystals soaked in a cryoprotectant solution containing 20% glycerol and cooled to 100 K in a nitrogen gas stream. The diffraction data were integrated and scaled with the HKL2000 program package []. Crystal structures were solved by the molecular replacement method using the program MOLREP [] with the published structure of ALG-2 (PDB ID 1HQV and 2ZN8) as a search model for des3-23ALG-2ΔGF122 and des3-20ALG-2F122A. All models were refined with the programs CNS [] and REFMAC5 in the CCP4 package []. Manual adjustments of the model were performed with COOT []. All of the structural figures were generated with PyMol (DeLano Scientific LLC, Palo Alto, CA). Rmsd was calculated with the program lsqkab in the CCP4 package []. Inter-helix angles and distances of EF-hand motifs were estimated by using vector geometry mapping (VGM) software [] downloaded from URL: […]

Pipeline specifications

Software tools Molrep, CNS, REFMAC5, Coot, PyMOL
Applications Small-angle scattering, Protein structure analysis
Organisms Dipturus trachyderma, Homo sapiens
Diseases Aortic Valve Insufficiency, Neoplasms