Computational protocol: MHC Class I Bound to an Immunodominant Theileria parva Epitope Demonstrates Unconventional Presentation to T Cell Receptors

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Protocol publication

[…] The structure was determined by molecular replacement using HLA-B*5703 (2BVO.pdb) as a search model in AMoRe . Initial rigid body refinement was followed by a series of restrained TLS refinements performed using REFMAC to Rwork of 19.9% and Rfree 23.9%. Manual rebuilding was carried out in COOT . Continuous density allowed unambiguous model building of N*01301. No density was visible for the N-terminal His tag or the C-terminal biotinylation signal, which are presumably flexible. Crystallographic statistics for the final models are given in . All figures of molecular models and electron density were generated in PyMol supplied by Delano Scientific LLC (www.pymol.org) and electrostatic potential was calculated using APBS through the Pymol interface. The atomic coordinates and structure factors are deposited in the Protein Data Bank (www.pdb.org): ID code 2xfx (coordinates) r2xfxsf (structure). […]

Pipeline specifications

Software tools Coot, PyMOL
Application Protein structure analysis
Organisms Mus musculus, Theileria parva, Bos taurus
Diseases Lymphoproliferative Disorders