Table I. Data collection and refinement statistics Statistics HLA-B*3501 HLA-B*3508 Data collection Temperature (K) 100 Space group P212121 Cell dimensions (a,b,c) (Å) 50.81, 81.56, 110.38 Resolution (Å) 50–2 Total number of observations 115,720 Number of unique observations 28,293 Multiplicity 4.1 Data completeness (%) 88 (82.9) Number of data 2 I 72.4 I/ I 21.4 (3.9) Rmergea (%) 9.7 (42) Refinement Nonhydrogen atoms Protein 3160 Water 342 Resolution (Å) 2 Rfactorb (%) 21.3 Rfreeb (%) 23.33 Rms deviations from ideality Bond lengths (Å) 0.007 Bond angles ( ) 1.43 Impropers ( ) 25.05 Dihedrals ( ) 0.98 Ramachandran plot (%) Most-favored region 90.7 Allowed region 9.3 B-factors (Å2) Average main chain 29.52 Average side chain 31.86 Average water molecule 43.04 Rmsd of bonded Bs 1.76 100 P212121 50.83, 81.53, 110.73 50–1.8 158,895 43,173 3.7 99.1 (97.7) 81.7 31.7 (2.82) 4.3 (49.5) 3185 516 1.8 20.85 23.42 0.005 1.24 24.96 0.88 91.8 8.2 27.02 29.73 42.55 1.76 abRRmfaecrtgoer h|kl I|hk|l Fo | Ih|klFc |||// Ihhkkll.| Fo | for all data except 4% that were used for Rfree calculation. ever, it is the loss of the heavy chain interaction with the P3- Gln that considerably affects the peptide conformation. This polymorphism-induced change in peptide interactions cul- minates in a dramatic shift of residues P4-Pro, P5-Ala, and P6-Pro of the peptide (Fig. 5, C and D). The side chain of P3-Gln within the HLA-B*3501–APQP complex swings upwards, forming H bonds to P5-AlaN and P5-AlaO. To ac- commodate the new conformation of the P3-Gln, the P4- Pro is pushed away toward the 1 helix of HLA-B*3501. The movement of the P4-Pro also includes a dramatic flip in the main chain carbonyl group P4-Pro peptide main chain, which then results in a marked shift in the main chain con- formation of P5-Ala, such that the P5-Ala C groups are 6.5 Å apart in the HLA-B*3501 and HLA-B*3508 structures. This JEM VOL. 202, November 7, 2005 A R T I C L E Figure 6. Local impact of the 156 polymorphism on peptide pre- sentation. (A) An extensive network of H bonding is seen involving Arg 156 in HLA-B*3508. Particularly important is the interaction with P3-Gln. (B) The polymorphic residue, Leu 156, makes no direct contacts with the peptide in HLA-B*3501. The side chain of P3-Gln interacts instead by pushing P4-Pro toward the 1 helix and pulling P5-Ala and P6-Pro in the direction if the 2 helix. Particularly evident is the switch from cis–P6-Pro to trans–P6-Pro. Residues are in ball-and-stick format. Polar interactions are depicted as dotted lines. The polymorphic residue is green, the peptide is yellow, and other MHC heavy chain residues are shown in gray. change in peptide conformation also moves the P5-Ala and P6-Pro closer toward the 2 helix of HLA-B*3501 (Fig. 5 D) and results in a switch from cis–P6-Pro to trans–P6-Pro. These conformational changes are important enough to drastically reduce recognition of the HLA-B*3501–APQP complex by the majority of T cells raised against HLA- B*3508–APQP. CTLs specific for the APQP epitope interact with peptide residues that are oriented differently when bound to HLA- B*3501 and HLA-B*3508 To investigate why these peptide structural differences had such a major impact on CTL recognition, three APQP-spe- cific CTL clones raised from the HLA-B*3508 donor SB 1255