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Crystal structure of a non-canonical high affinity peptide complexed with MHC class I: a novel use of alternative anchors.

Apostolopoulos V, Yu M, Corper AL, Li W, McKenzie IF, Teyton L, Wilson IA, Plebanski M

  • Journal Journal of molecular biology

  • Published 02 Jul 2002

  • Volume 318

  • ISSUE 5

  • Pagination 1307-16

  • DOI 10.1016/s0022-2836(02)00198-5


The crystal structure of a non-standard peptide, YEA9, in complex with H-2Kb, at 1.5 A resolution demonstrates how YEA9 peptide can bind with surprisingly high affinity through insertion of alternative, long, non-canonical anchors into the B and E pockets. The use of "alternative pockets" represents a new mode of high affinity peptide binding, that should be considered when predicting peptide epitopes for MHC class I. These novel interactions encountered in this non-canonical high affinity peptide-MHC complex should help predict additional binding peptides from primary protein sequences and aid in the design of alternative approaches for peptide-based vaccines.