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MHC molecules evolved with the descent of jawed fishes some 350-400 million years ago. However, very little is known about the structural features of primitive MHC molecules. To gain insight into these features, we focused on the MHC class I Ctid -UAA of the evolutionarily distant grass carp ( Ctenopharyngodon idella ). The Ctid -UAA H chain and β2-microglobulin ( Ctid -β2m) were refolded in vitro in the presence of peptides from viruses that infect carp. The resulting peptide- Ctid -UAA (p/ Ctid -UAA) structures revealed the classical MHC class I topology with structural variations. In comparison with known mammalian and chicken peptide-MHC class I (p/MHC I) complexes, p/ Ctid -UAA structure revealed several distinct features. Notably, 1) although the peptide ligand conventionally occupied all six pockets (A-F) of the Ag-binding site, the binding mode of the P3 side chain to pocket D was not observed in other p/MHC I structures; 2) the AB loop between β strands of the α1 domain of p/ Ctid -UAA complex comes into contact with Ctid -β2m, an interaction observed only in chicken p/BF2*2101-β2m complex; and 3) the CD loop of the α3 domain, which in mammals forms a contact with CD8, has a unique position in p/ Ctid -UAA that does not superimpose with the structures of any known p/MHC I complexes, suggesting that the p/ Ctid -UAA to Ctid -CD8 binding mode may be distinct. This demonstration of the structure of a bony fish MHC class I molecule provides a foundation for understanding the evolution of primitive class I molecules, how they present peptide Ags, and how they might control T cell responses.

The Structure of the MHC Class I Molecule of Bony Fishes Provides Insights into the Conserved Nature of the Antigen-Presenting System