Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 99, Issue 13, Pages 8820-8825Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.132272099
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Funding
- NIAID NIH HHS [R01 AI017134, AI-18785, R56 AI017134, P01 AI022295, AI-17134, R01 AI018785, R37 AI018785, R56 AI018785, AI-22295] Funding Source: Medline
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We have solved the crystal structure of the MHCII molecule, [Ab, containing an antigenic variant of the major [Ab-binding peptide derived from the MHCII IEalpha chain. The four MHC pockets at p1, p4, p6, and p9 that usually bind peptide side chains are largely empty because of alanines in the peptide at these positions. The complex is nevertheless very stable, apparently because of unique alternate interactions between the IA(b) and peptide. In particular, there are multiple additional hydrogen bonds between the N-terminal end of the peptide and the IA(b) alpha chain and an extensive hydrogen bond network involving an asparagine at p7 position of the peptide and the IA(b) beta chain. By using knowledge of the shape and size of the traditional side chain binding pockets and the additional possible interactions, an IA(b) peptide-binding motif can be deduced that agrees well with the sequences of known IA(b)-binding peptides.
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