Fig. 3: Crystal structures of dsA2 in complex with dipeptides in the A and F pockets. | Nature Communications

Fig. 3: Crystal structures of dsA2 in complex with dipeptides in the A and F pockets.

From: Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection

Fig. 3

a Overlay of the peptide-binding groove with a ribbon diagram of dsA2/GL in gold and wtA2/GLCPLVAML in gray. The C84-C139 disulfide bond is shown as sticks. b The dsA2/GM2 structure (gold; see Supplementary Table 2) is shown overlaid with the published wtA2/GLCPLVAML structure (pdb 3MRF; gray). View from the side of the α2 helix with comparison of the GLCPLVAML peptide (gray) with the GM dipeptides (cyan) in the A and F pocket (peptides depicted as sticks). A transparent cartoon of the secondary structures of the peptide-binding groove is shown for orientation. c, d Zoom into the F pocket of the same structure, showing that the carboxylate group of the GM dipeptide is in the same orientation as the carboxyl group of the full-length peptide, despite the Tyr84Cys mutation. In dsA2/GM2, water molecules (W1, W2, W3, and W4) fill the space where the side chain of Tyr84 is pointing in wtA2/GLCPLVAML.

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