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. 2023 Aug 18;14:5020. doi: 10.1038/s41467-023-40736-6

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2023

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Fig. 1 — a Top panel, superimposition of bound (RA)₆FAKKKYCL (cyan) and (RA)₆FVKKKYCL (yellow) 20mer peptides. The backbone and side chain conformations of the peptides overlap between P3 and P8 but differ at P1, P2, and P-1 (P-2 was visible only in 20mer FV). Bottom panel, superimposition of bound 20mer peptides with 8mer FAKKKYCL (pink) and FVKKKYCL (green) control peptides. The four peptides overlap between P3 and P8 and are most divergent at P1. b Interactions in the A pocket show that the main-chain nitrogen of P1 Phe FV 20mer (top panel) and FA 20mer (bottom panel) has rotated and formed a hydrogen bond with Asn63 (black dashed lines). The main-chain carbonyl oxygen in FV 20mer hydrogen bonds with Tyr159 and Tyr7, while the same atom in FA 20mer has undergone a very unusual rotation toward the α1-helix and forms no interaction with MHC I residues. In both panels, extension residues protrude out of the groove. c In the 20mer structures, the side chains of Arg62 have moved out of the canonical positions seen in 8mer structures, which opens the A pocket and allows the extension residues (RA)₆ to exit out.