Highly divergent T-cell receptor binding modes underlie specific recognition of a bulged viral peptide bound to a human leukocyte antigen class I molecule

HLA-I molecules can present long peptides, yet the mechanisms by which TCRs recognise featured pHLA-I landscapes are unclear. We compared the binding modes of three distinct human TCRs, CA5, SB27 and SB47, complexed with a super-bulged viral peptide (LPEPLPQGQLTAY) restricted by HLA-B*35:08. The CA5 and SB27 TCRs engaged HLA-B*35:08LPEP similarly, straddling the central region of the peptide but making limited contacts with HLA-B*35:08. Remarkably, the CA5 TCR did not contact the alpha1-helix of HLA-B*35:08. Differences in the CDR3beta loop between the CA5 and SB27 TCRs caused altered fine specificities. Surprisingly, the SB47 TCR engaged HLA-B*35:08LPEP using a completely distinct binding mechanism, namely bypassing the bulged peptide and making extensive contacts with the extreme N-terminal end of HLA-B*35:08. This docking footprint included HLA-I residues not observed previously as TCR contact sites. The three TCRs exhibited differing patterns of alloreactivity towards closely related or distinct HLA-I allotypes. Thus, the human T-cell repertoire comprises a range of TCRs that can interact with bulged pHLA-I epitopes using unpredictable strategies, including the adoption of atypical footprints on the MHC-I.