Figure 4.

PUB-HS CDR3β AA-sequences show conserved regions and regions with high variability. The levenshtein distance was calculated (i.e. substitution, deletions or insertions of AAs) between CDR3β AA-sequences that express the same TRBV/TRBJ-genes as the PUB-I CDR3β AA-sequence. PUB-HS CDR3β AA-sequences were included with 1, 2 and 3 AA-differences compared to the PUB-I CDR3β AA-sequence. Sequence logos generated using WebLogo (http://weblogo.berkeley.edu/logo.cgi) show the relative frequency of each AA at each given position. The junctional regions (AAs that do not align with the germline TRBV or TRBJ-gene) are shown within the dotted-line box. (A) The CDR3β AA-sequences specific for HLA-A*02:01-restricted EBV-LMP2^FLY with a CDR3 length of 14 and 15 AAs were stacked and show conserved and variable regions in the CDR3β-region. (B) Shown are the CDR3 length distributions of CDR3β AA-sequences specific for EBV-LMP2^FLY-expressing TRBV6-5/TRBJ1-2. (C) Shown are representative examples of PUB-HS (1, 2 or 3 AA differences) and PUB-I CDR3β AA-sequences that were stacked per specificity and TRBV/TRBJ-usage.