Nonclassical binding of formylated peptide in crystal structure of the MHC class Ib molecule H2-M3

Cell. 1995 Aug 25;82(4):655-64. doi: 10.1016/0092-8674(95)90037-3.


H2-M3 is a class Ib MHC molecule of the mouse with a 10(4)-fold preference for binding N-formylated peptides. To elucidate the basis of this unusual specificity, we expressed and crystallized a soluble form of M3 with a formylated nonamer peptide, fMYFINILTL, and determined the structure by X-ray crystallography. M3, refined at 2.1 A resolution, resembles class la MHC molecules in its overall structure, but differs in the peptide-binding groove. The A pocket, which usually accommodates the free N-terminus of a bound peptide, is closed, and the peptide is shifted one residue, such that the P1 side chain is lodged in the B pocket. The formyl group is coordinated by His-9 and a bound water on the floor of the groove.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • DNA, Complementary / genetics
  • Electrochemistry
  • Histocompatibility Antigens Class I / chemistry*
  • Histocompatibility Antigens Class I / genetics
  • Histocompatibility Antigens Class I / metabolism*
  • In Vitro Techniques
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • N-Formylmethionine / metabolism
  • Oligopeptides / chemistry
  • Oligopeptides / genetics
  • Oligopeptides / metabolism*
  • Protein Binding
  • Protein Conformation


  • DNA, Complementary
  • Histocompatibility Antigens Class I
  • Oligopeptides
  • N-Formylmethionine