Fig. 2

DQ6-binding cores in prepro-HCRT and their structural impacts. a Thirty overlapping peptides covering prepro-HCRT were added, individually, into a reaction containing soluble DQ6, bio-EBV_486–500 peptide, and HLA-DM (a peptide loading catalyst). DQ6-associated bio-EBV_486–500 was measured at steady state by ELISA³¹. %Competition = 1−%DQ6/EBV binding. Strong (>75%Competition, in colors) and weak (50–75%Competition, in gray) DQ6 binders with predicted cores (bolded) are aligned. Data are represented as mean ± SEM (standard error of the mean); n = 4. b Top view of HCRT_56–69 (orange) in the peptide-binding groove of DQ6 (α/β, light green/blue surface, PDB: 6DIG). Core residues are indicated. c Alignment of DQ6-HCRT_56–69 (α/β, light green/blue cartoon; peptide, orange stick) and DQ6-HCRT_1–13 structures³⁴ (α/β, dark green/blue; peptide, magenta) illustrating three regions in DQ6 with noticeable conformation differences (detailed in Supplementary Fig. 1e). d Side view of DQ6 (β chain removed to reveal peptides) in complex with HCRT_1–13 (PDB: 1UVQ) and DQ6-HCRT_56–69 (PDB: 6DIG) and models of HCRT_25–37 and HCRT_87–100 (sticks in the same color as in a). Arrow indicates predicted positioning for interaction of TCRα/β CDR3s. e Zoom-in of the 9-aa core registers of peptides shown in d. Arrows indicate TCR (up) or DQ6 (down) facing resides