Figure 3. Increased ratios of germline-encoded to recombined peptide contacts in PIT-matched TCRs.

A) Gaussian Surface representation of a model of Clone 640, a PIT-matching TCR with a 10 AA TRA junction (7 CDR contacts) paired with a 12 AA TRB junction (8 CDR contacts), that binds the GAD65 113–132 peptide ⁵⁶ presented by the HLA DRB1*0401 class II molecule ¹³. The viewing plane is from the interface with the MHC molecules, which together with the peptide, have been removed from the representation for clarity. Labels indicate the CDR loops, with letters denoting the chain (α or β); and numbers, the CDR loop. Numbers in parentheses are the number of predicted peptide contacts with the CDR loop. B) A model of Clone 2353, a PIT-non-matching TCR with a 17AA TRA junction (7 CDR contacts) paired with a 14 AA TRB junction (8 CDR contacts), that binds the IGRP305–324 peptide presented by the HLA DRB1*0401 class II molecule. C) The number of total peptide contacts for either the TRA or TRB chains did not differ significantly between PIT-matched and PIT-non-matched TCRs (p-value >0.05, Wilcox test). D) Ratios of TRA CDR1 to CDR3 peptide contacts decreased significantly with increasing TRA junction length. ****, p-value < 1e-4 for a slope of 0, calculated using linear modeling.