Fig. 5: Superposition of the unlocked and locked states of the F pocket and comparison of the electrostatic surface of the peptide-free and -occupied dsA2 molecules. | Nature Communications

Fig. 5: Superposition of the unlocked and locked states of the F pocket and comparison of the electrostatic surface of the peptide-free and -occupied dsA2 molecules.

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

Fig. 5

a The unlocked state (derived from the dsA2/peptide_free-1 structure) is in gold, and the locked state (from the dsA2/NLVPMVATV structure) in cyan. The side chains involved in locking the F pocket are His74, Asp77, Arg97, His114, and Tyr116. The adjacent residues involved in locking the A pocket (Phe9, His70, and Tyr99) are also depicted to show their close proximity. b Top view of the F pocket in the unlocked state showing that the conformations of the side chains of the peptide-free dsA2 molecule coincide with the side chain conformations of one of the conformational states of dsA2/GM2 structure, where the methionine side chain is not involved in interactions with the side chains lining the F pocket. The only difference is a hydrogen bond between His74 and Asp77 in the peptide-free dsA2 structure (yellow dotted line). c Electro-surface potential of the peptide-binding groove of peptide-loaded dsA2 (+NV9), dsA2/GM2 (+GM), and peptide-free dsA2 (empty). The A and F pockets are marked to show their opening up, and the accompanying charge shifts, in the unlocked state.

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