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 ( and electrostatic potential was calculated using APBS through the Pymol interface. The atomic coordinates and structure factors are deposited in the Protein Data Bank ( 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