Computational protocol: Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove

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Protocol publication

[…] Thin plate-like crystals were obtained for HLA-A*02:01 complex with UFP (16–26) in 30% PEG 5000 MME, 0.1 M Tris-HCl pH 8.0, 0.2 M lithium sulfate and HLA-A*02:01 complex with UFP (16–27) in 30% PEG 4000, 0.1 M Tris-HCl pH 8.0, 0.2 M lithium sulfate. Crystals were obtained by sitting drop vapor diffusion by mixing 0.15 μl protein and 0.15 μl of precipitant at 20°C after 2–4 days. The crystals were flash frozen in cryoprotectant (Reservoir solution: 100% glycerol - 3:1) using liquid nitrogen. Diffraction data for HLA-A2/ UFP (16–26) and HLA-A2/ UFP (16–27) were collected remotely at beamline 7.1 at the Stanford Synchrotron Radiation Light source (SSRL) and processed to 1.8 Å and 1.5 Å resolution, respectively using HKL2000 (). Phases were obtained using the protein coordinates for HLA-A2 (PDB ID 3MRE) using molecular replacement with Phaser MR () in ccp4i (; ) and provided unambiguous electron density for both the peptides. Model building was carried out using COOT (; ). Structures were refined using Refmac () to a final Rwork/Rfree of 0.164/0.222 for HLA-A2/UFP (16–26) (PDB ID 5D9S) and Rwork/Rfree of 0.195/0.219 for HLA-A2/UFP (16–27) (PDB ID 5DDH). […]

Pipeline specifications

Software tools PHENIX, Coot
Application Protein structure analysis
Organisms Toxoplasma gondii