Structure‐guided stabilization of pathogen‐derived peptide‐HLA‐E complexes using non‐natural amino acids conserves native TCR recognition

The nonpolymorphic class Ib molecule, HLA‐E, primarily presents peptides from HLA class Ia leader peptides, providing an inhibitory signal to NK cells via CD94/NKG2 interactions. Although peptides of pathogenic origin can also be presented by HLA‐E to T cells, the molecular basis underpinning their role in antigen surveillance is largely unknown. Here, we solved a co‐complex crystal structure of a TCR with an HLA‐E presented peptide (pHLA‐E) from bacterial (Mycobacterium tuberculosis) origin, and the first TCR‐pHLA‐E complex with a noncanonically presented peptide from viral (HIV) origin. The structures provided a molecular foundation to develop a novel method to introduce cysteine traps using non‐natural amino acid chemistry that stabilized pHLA‐E complexes while maintaining native interface contacts between the TCRs and different pHLA‐E complexes. These pHLA‐E monomers could be used to isolate pHLA‐E‐specific T cells, with obvious utility for studying pHLA‐E restricted T cells, and for the identification of putative therapeutic TCRs.