The Structure of HLA-DM, the Peptide Exchange Catalyst that Loads Antigen onto Class II MHC Molecules during Antigen Presentation Lidia Mosyak, Dennis.

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The Structure of HLA-DM, the Peptide Exchange Catalyst that Loads Antigen onto Class II MHC Molecules during Antigen Presentation Lidia Mosyak, Dennis M. Zaller, Don C. Wiley Immunity Volume 9, Issue 3, Pages 377-383 (September 1998) DOI: 10.1016/S1074-7613(00)80620-2

Figure 1 Comparison of the Structures of HLA-DM, HLA-DR1, and FcRn, the Neonatal Fc Receptor (A) DM (yellow), DR1 (red), disulfide bonds (green). The locations of tryptophans α62 and β120 are labeled with arrows. (B) Superposition of the α1 and β1 domains of HLA-DM (yellow) and HLA-DR1 (red). (rmsd = 2.5 Å for 160 Cα pairs). (C) Superposition of the α1 and β1 domains of HLA-DM (yellow) and α1 and α2 domains of FcRn (gray) (rmsd = 2.4 Å for 153 Cα pairs). (D) Superposition of the α2 and the β2 domains of HLA-DM (yellow) and HLA-DR1 (red) (α2 domain, rmsd = 1.04 Å for 92 Cα pairs; β2 domain, rmsd = 2.1 Å for 93 Cα pairs). Immunity 1998 9, 377-383DOI: (10.1016/S1074-7613(00)80620-2)

Figure 2 Helical Packing in HLA-DM (A) Three segments of the helical region pack differently. At each end of the domains the helices contact each other with nonpolar residues; in the middle is a deep pocket of polar residues. At the bottom of the cavity, both Glu α35 and Asp α68 are within hydrogen bonding distance of His α20. The hydroxyl group of Ser β9 could be rotated to hydrogen bond directly to His α20 but in the structure is hydrogen bonded through a water molecule to His α20. (B) Surface representation of HLA-DM (same viewpoint as in [A]). Arrow shows central deep pocket, also shown in detailed dot surface. (C) Surface representation of HLA-DR1 (with bound peptide omitted). Peptide side chain binding pockets between the α helices are labeled. Immunity 1998 9, 377-383DOI: (10.1016/S1074-7613(00)80620-2)

Figure 3 Conserved Hydrogen Bonds between CLIP and HLA-DR3 Dashed lines show hydrogen bonds between peptide backbone atoms found on all bound peptides and residues conserved in all class II molecules, shown for HLA-DR3/CLIP (Ghosh et al. 1995). Hydrogen bonds made by peptide positions 1, −1, and −2 (numbered as in Stern et al. 1994) are labeled P1, P-1, and P-2. Immunity 1998 9, 377-383DOI: (10.1016/S1074-7613(00)80620-2)