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Volume 7, Issue 4, Pages 473-481 (October 1997) X-Ray Crystal Structure of HLA-DR4 (DRA*0101, DRB1*0401) Complexed with a Peptide from Human Collagen II Andréa Dessen, C.Martin Lawrence, Susan Cupo, Dennis M. Zaller, Don C. Wiley Immunity Volume 7, Issue 4, Pages 473-481 (October 1997) DOI: 10.1016/S1074-7613(00)80369-6

Figure 1 Ribbon Diagram of the HLA-DR4/CII(1168–1180)/SEB Complex Peptide atoms are shown as balls and sticks. Two loops from SEB that are not visible in electron density maps are represented by dotted lines. Immunity 1997 7, 473-481DOI: (10.1016/S1074-7613(00)80369-6)

Figure 2 CII(1168–1180) Peptide in the HLA-DR4 Binding Site Overlaid with an Fo-Fc Omit Map Contoured at 2.2 σ Collagen peptide atoms were omitted from electron density map calculation. Gln at P −2, Gln at P5, and Leu at P10 were modeled as Ala. Immunity 1997 7, 473-481DOI: (10.1016/S1074-7613(00)80369-6)

Figure 3 CII(1168–1180) Peptide in the HLA-DR4 Binding Site (A) CII(1168–1180) peptide in the HLA-DR4 binding site. P1 Met (green) fits into a deep pocket. Asp P4 and Lys-β71 interact in pocket 4. P-2, P5, and P10 are displayed as Ala. (B) Hydrogen bonds between CII(1168–1180) and HLA-DR4. Peptide side chains are shown as Ala, with the exception of Asp P4. Ten hydrogen bonds are made from the peptide main chain to conserved class II residues. Lys-β71 makes two other hydrogen bonds, one to the P4 Asp side chain and another to the carbonyl of P5. Immunity 1997 7, 473-481DOI: (10.1016/S1074-7613(00)80369-6)

Figure 4 Interactions in the P4 Pockets of HLA-DR1, HLA-DR4 (DRB1*0401), and HLA-DR4 (DRB1*0402) (A) Interatomic contacts in the P4 pocket of DR4/CII(1168–1180). Six hydrogen bonds are found in the pocket, including the one to a bound water molecule. Other residues forming the shared epitope are shown in yellow. (B) Pocket 4 of the DR1/HA complex. (C) Hypothetical model of pocket 4 of DRB1*0402, an HLA-DR4 allele that is not associated with the development of arthritis. Immunity 1997 7, 473-481DOI: (10.1016/S1074-7613(00)80369-6)

Figure 5 Comparison of DR1/HA, DR3/CLIP, and DR4/CII(1168–1180) Superposition of DR1/HA (yellow), DR3/CLIP (blue), and DR4/CII (1168–1180) (red) shows small structural differences in the α helix of the β1 domains. Immunity 1997 7, 473-481DOI: (10.1016/S1074-7613(00)80369-6)

Figure 6 Conformations of Peptides in the Binding Sites of MHC Class II Molecules (A) Hypothetical model of CII(261–273) peptide in the HLA-DR4 binding cleft. Phe-263 fits into the P1 pocket, and Glu (P4) hydrogen bonds to β71. (B) The conformations of five peptides observed in complexes with human and murine class II MHC molecules: DR1/HA (green), DR3/CLIP (purple), DR4/CII(1168–1180) (yellow), Iek/HB (red), and Iek/HSP70 (blue). The MHC class II molecules were superimposed to reveal the superposition of the peptides. View is approximately with MHC to the left and TCR to the right. Immunity 1997 7, 473-481DOI: (10.1016/S1074-7613(00)80369-6)