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The 2A3-D NKT TCR was isolated from a library expressing modified Vβ6 chains in which the CDR2β loop had been replaced with the corresponding sequence found in the Vβ8.2 CDR2β loop, such as to provide the appropriate contact residues important for CD1d recognition. The two tyrosine residues (βY46 and βY48) of the modified CDR2β loop converged on the same region of CD1d, with βY46 forming H-bonds with E83 and a salt bridge with K86, and βY48 sitting against M87 and H-bonding to E83. Furthermore, βE54 H-bonded to the main chain of CD1d and formed a salt bridge with K86; collectively these interactions were comparable to that previously observed in the Vβ8.2 NKT TCR-αGC-CD1d complex. The buried surface area of the autoreactive NKT TCR CD1d-complex was 940 Å2, compared to that of 760 Å2 of the Vβ8.2 NKT TCR-CD1d complex. Notably, while the CDR3β loop of the NKT TCR has previously been shown to play at most a minor role in contacting CD1d, for the 2A3-D NKT TCR, it played a more prominent role, exclusively interacting with CD1d, positioned away from the PI head group.
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