Figure 3 - full size

 

Figure 3.
Fig. 3. A type II -turn at the C-terminal region of the Gag[PP16] peptide. (A) C-terminal region of the DR1 peptide-binding site with bound Gag[PP16] peptide showing conserved MHC peptide hydrogen bonds. Conserved MHC peptide hydrogen bonds in this region are shown as gray dashed lines, with the Gag[PP16] intraturn hydrogen bond between the nitrogen of Ala (P12) and the carbonyl oxygen of Ser (P9) shown as a red dashed line. (B) Closeup view of the Gag[PP16] hairpin, showing the intraturn hydrogen bond and - values characteristic of a type II -turn. (C) Alignment of HLA-DR crystal structures exhibiting ordered peptide density beyond P10. Complexes were aligned by least-squares fitting of 1 and 1 domains. Peptides are shown as C traces. DR1/TP1 is red (PDB ID code 1KLU [PDB] ), DR2a/MBP is blue (PDB ID code 1FV1 [PDB] ), DR3/CLIP is magenta (PDB ID code 1A6A [PDB] ), DR1/Ha is cyan (PDB ID code 1DLH [PDB] ), DR2a/EBV is gray (PDB ID code 1H15 [PDB] ), and DR4/collagen is orange (PDB ID code 2SEB [PDB] ).