HLAI polymorphisms contribute to differences in the fine presentation mode of RM9-Nef. Comparison of the presentation modes of HLA-B*07:02-RM9 (green sticks), HLA-B*81:01-RM9 (orange sticks), HLA-B*42:01-RM9 (yellow sticks) and HLA-B*42:02-RM9 (pink sticks), the HLAI binding groove is shown as grey cartoon. (A) Structural alignment of HLA-B*07:02-RM9, HLA-B*81:01-RM9, HLA-B*42:01-RM9 and HLA-B*42:02-RM9 peptide conformations showing differences around peptide residues Arg1, Leu6 and Arg7 (black arrows pointing up indicate that the corresponding residue is solvent exposed and available for TCR contact, black arrows pointing down indicate that the corresponding residue is buried in the HLA groove; no arrow indicates a position between solvent exposed and buried). The position of the circled residue (Leu6) may be important to explain differential escape when presented by different HLAIs. (B) RM9-Nef residue Leu6 undergoes a 3 Å shift in position in the HLA-B*81:01 structure compared to HLA-B*42:01 and HLA-B*42:02. (C) HLA-B*81:01 contains a Leu at position 156 compared to Arg in HLA-B*07:02 and Asp in HLA-B*42:01 and HLA-B*42:02. This polymorphism alters the interactions between RM9-Nef residue Leu6 and the different HLAIs contributing towards its conformational heterogeneity. (D) HLA-B*81:01 contains a Leu at position 147 compared to Trp in HLA-B*07:02, HLA-B*42:01 and HLA-B*42:02. This polymorphism reduces the interactions between residues Pro8 and Met9 in the peptide and HLA-B*81:01 compared to the other HLAIs. (E) HLA-B*42:02 contains a His at position 9 compared to Tyr in HLA-B*07:02, HLA-B*81:01 and HLA-B*42:01. This polymorphism reduces the interactions between residue Pro2 in the peptide and HLA-B*42:02 compared to the other HLAIs.