A murine MHC-Ib molecule, H2-Q9, drives peptide-centric T cell receptor recognition of a viral antigen

Highly polymorphic classical major histocompatibility complex class I (MHC-Ia) molecules present peptides to T cell receptors (TCRs) expressed on CD8⁺ T cells. In contrast, non-classical MHC-Ib molecules are less polymorphic, and the structural principles governing their recognition by TCRs remains poorly understood. H2-Q9, a murine Qa-2 family MHC-Ib molecule presents the mouse polyomavirus-derived VP2.139 peptide (HALNVVHDW) to CD8⁺ T cells, yet the molecular basis of TCR recognition of H2-Q9/peptide complexes remains unclear. Here, we characterised the interactions of two VP2.139-specific TCRs, C3K and AH1, with the VP2.139 peptide presented by H2-Q9, which showed similar moderate binding affinities. We then determined the structure of the TCR C3K bound to the VP2.139 peptide presented by H2-Q9. TCR C3K adopted a diagonal docking orientation and was tilted toward the N-terminal end of the peptide. The CDR3 loops formed extensive contacts with peptide positions P1-P8, whereas alanine-scanning mutagenesis at positions P1-P7 impaired TCR recognition. Structural comparison of H2-Q9 with classical murine MHC-Ia molecules identified substitutions in the α3-domain that alter the CD8-binding interface and may explain the previously observed absence of CD8 binding to H2-Q9. Together, these findings provide insight into antigen recognition by a monomorphic MHC-Ib molecule.