Volume 1, Issue 4, Pages 531-541 (March 1998) Structural Features Impose Tight Peptide Binding Specificity in the Nonclassical MHC Molecule HLA-E  Christopher A. O'Callaghan, José Tormo, Benjamin E. Willcox, Veronique M. Braud, Bent K. Jakobsen, David I. Stuart, Andrew J. McMichael, John I. Bell, E.Yvonne Jones  Molecular Cell  Volume 1, Issue 4, Pages 531-541 (March 1998) DOI: 10.1016/S1097-2765(00)80053-2

Figure 1 Overview of the Structure of HLA-E The heavy chain is shown in green, β2-microglobulin in light blue, and the peptide in darker blue. The α1 helix is on the right and the α2 helix on the left. Molecular Cell 1998 1, 531-541DOI: (10.1016/S1097-2765(00)80053-2)

Figure 2 View of the Class Ia Leader Peptide Bound in the HLA-E Groove A Connolly molecular surface (Connolly 1983) for the heavy chain is shown in green and the pockets are labeled (A)–(E). The peptide is oriented with the N terminus at the left of the picture in the A pocket, and the Cα atoms from each residue are numbered P1–P9. Molecular Cell 1998 1, 531-541DOI: (10.1016/S1097-2765(00)80053-2)

Figure 3 The Peptide Pockets in HLA-E The key residues for each pocket at the designated peptide positions are shown as space filling van der Waal surfaces with views looking into the pocket. The atoms are coloured by atom type (carbon grey, nitrogen blue, oxygen red, sulphur yellow) and bonds in the peptide are shown as light blue in the main chain and white in the sidechains. The top left hand labels refer to the pockets and the bottom right hand labels in green refer to the peptide positions (VMAPRTVLL). Molecular Cell 1998 1, 531-541DOI: (10.1016/S1097-2765(00)80053-2)

Figure 5 Stereo Comparison with Class Ia Structures (A) Comparative peptide main-chain conformations. HLA-E is shown in red, HLA-B8 (PDB accession code: 1AGD) in yellow, HLA-B35 (1A1N) in orange, HLA-B53 (1A1O, 1A1M) in purple, H-2Kb (1VAA, 1VAB, 1VAC, 1VAD) in green and HLA-A2 complexes (1HHG, 1HHH, 1HHI, 1HHJ, 1HHK, 2CLR) in light blue. Superpositions were performed using the α1 and α2 domains of the molecules and the peptides are viewed from the α2 helix side of the groove. (B) Superposition of HLA-E and HLA-A2. HLA-E is shown in red and HLA-A2 in light blue, with peptides for the various structures coloured as above. Molecular Cell 1998 1, 531-541DOI: (10.1016/S1097-2765(00)80053-2)

Figure 4 Hydrogen Bonds to the Peptide in HLA-E Hydrogen bonds to the peptide main chain are shown as pink dashed lines. The peptide side chains have been omitted for clarity and the peptide residues are labelled where a hydrogen bond is formed in the mid portion of the peptide. Molecular Cell 1998 1, 531-541DOI: (10.1016/S1097-2765(00)80053-2)

Figure 6 Key Residues in the Floor of the HLA-E Groove The landmark residues in the floor of the groove are shown. Hydrogen bonds involving His-9 and His-99 are shown as pink dashed lines and the position of the peptide main chain is shown in red. Molecular Cell 1998 1, 531-541DOI: (10.1016/S1097-2765(00)80053-2)

Figure 7 Residues Differing between HLA-E and Qa-1b The Cα atoms of residues that differ between the two molecules are represented as small spheres and colored green if the side chains point into the groove in HLA-E and orange if they do not. Molecular Cell 1998 1, 531-541DOI: (10.1016/S1097-2765(00)80053-2)