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

J Mol Biol. 2002 May 17;318(5):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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Antigen Presentation
  • Drosophila
  • Drug Design
  • Fungal Proteins / chemistry
  • Fungal Proteins / immunology
  • Histocompatibility Antigens Class I / chemistry*
  • Histocompatibility Antigens Class I / immunology
  • Models, Molecular
  • Peptides / chemistry*
  • Peptides / immunology
  • Protein Binding
  • Protein Conformation
  • Vaccines


  • Fungal Proteins
  • Histocompatibility Antigens Class I
  • Peptides
  • Vaccines

Associated data

  • PDB/1G7P