Disorder and T cell epitope prediction for EBV Nuclear Antigen 1. (a) PONDR® plot of the Epstein Barr Nuclear Antigen 1 protein (Swiss-Prot: P03211). The PPPGRPP epitope that induces cross-reactivity to an epitope on Sm B/B' is found in residues 398–412, almost exactly at the sharp minimum of the PONDR® plot. This is the only known cross-reacting epitope in the virus. (b) T cell epitopes of EBNA1 predicted by the ProPred server. Only the results for alleles HLA-DRB_01, HLA-DRB_0102, HLA-DRB1_0301, and HLA-DRB_0305 are shown. The remaining 47 alleles show a very similar picture. The threshold is set at 3%. The black bars delimit the strongly disordered regions of the PONDR® plot shown in (a). It is apparent that the highly disordered region of the first approximately 400 amino acids is predicted to be nearly devoid of potential T cell epitopes. The epitope from residues 398–412 that cross-reacts with the SmB protein is predicted to be most reactive with alleles HLA DRB5_0101 and DRB5_0105, although just slightly below a 3% threshold (data not shown).