Class II MHC molecules contain two different polypeptide chains, a 33-kDa a chain and a 28-kDa p chain, which associate by noncovalent interactions (see Figure 7-5b). Like class I a chains, class II MHC molecules are membrane-bound glycoproteins that contain external domains, a transmembrane segment, and a cytoplasmic anchor segment. Each chain in a class II molecule contains two external domains: a1 and a2 domains in one chain and pi and p2 domains in the other. The membrane-proximal a2 and p2 domains, like the membrane-proximal a3/p2-microglobulin domains of class I MHC molecules, bear sequence similarity to the im-munoglobulin-fold structure; for this reason, class II MHC molecules also are classified in the immunoglobulin super-family. The membrane-distal portion of a class II molecule is composed of the ai and pi domains and forms the antigen-binding cleft for processed antigen.
X-ray crystallographic analysis reveals the similarity of class II and class I molecules, strikingly apparent when the molecules are surperimposed (Figure 7-7). The peptide-binding cleft of HLA-DR1, like that in class I molecules, is composed of a floor of eight antiparallel p strands and sides of antiparallel a helices. However, the class II molecule lacks the conserved residues that bind to the terminal residues of short peptides and forms instead an open pocket; class I presents more of a socket, class II an open-ended groove. These functional consequences of these differences in fine structure will be explored below.
An unexpected difference between crystallized class I and class II molecules was observed for human DR1 in that the rf7 Ja.
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