Unveiling structural determinants of peptide recognition by public and private SARS-CoV-2-specific T-cell receptors

Public T cell receptors (TCRs) recurrently emerge across individuals in response to common pathogens, yet the structural and biophysical basis distinguishing public from private clonotypes remains incompletely defined. Here, we combine epitope mapping, single-cell TCR sequencing, and single-particle cryo-electron microscopy to dissect CD8⁺ T cell responses to the immunodominant SARS-CoV-2 ORF3a_(207-215) epitope presented by HLA-A*01:01. Among responding clonotypes, we identify a public TCR (TCR_pub), shared across donors, and a private TCR (TCR_priv) that uses nearly identical β chains but distinct α chains. Despite comparable micromolar affinities and functional avidities, cryo-EM structures at ~3 Å resolution reveal that the two receptors engage the peptide-MHC complex through distinct CDR-loop configurations and contact footprints. TCR_pub establishes contacts with the peptide and the MHC α2-helix primarily through the CDR2β and CDR3β loops, whereas TCR_priv distributes contacts across both MHC α-helices and engages the peptide via multiple CDR loops. In agreement with these observations, alanine-scanning mutagenesis reveals that TCR_pub shows greater sensitivity to peptide substitutions, consistent with its peptide-focused binding mode. These findings demonstrate how alternative α-chain pairing reconfigures the antigen-binding interface within a shared β-chain.