Structural Basis of Diverse Peptide Accommodation by the Rhesus Macaque MHC Class I Molecule Mamu-B*17: Insights into Immune Protection from Simian Immunodeficiency Virus

The development of an effective vaccine against HIV infection and AIDS is a global public health priority. Accordingly, there has been much scientific focus on SIV infection of nonhuman primates, especially rhesus macaques, which provides a useful model to inform HIV pathogenesis and study the efficacy of vaccine candidates (1, 2). In the past decade, most work on SIV-specific CD8⁺ T cell responses in the rhesus macaque model has centered on the MHC class I (MHC I) molecule Mamu-A*01 (3–20). More recently, however, the scope of immunological studies in this model has expanded to include additional MHC I molecules that display distinct biological properties. Mamu-B*17, which is present in >12% of captive Indian rhesus macaques (21), is associated with the control of SIV replication in vivo (22–26), although it should be noted that inheritance of this allele alone does not predict a favorable outcome and that the immunological basis for this association remains unclear. In humans, it is well-established that HLA-B*27 and HLA-B*57, the gene products of which present HIV-derived epitopes that elicit highly effective CD8⁺ T cell responses (27–31), are associated with reduced virus loads and delayed disease progression in HIV-infected individuals (27, 32–35). By analogy, the study of Mamu-B*17–positive rhesus macaques provides an opportunity to understand how specific MHC I molecules might impact AIDS virus replication in a controlled setting (31).

The peptide-binding specificity of Mamu-B*17 has been identified, together with a range of presented SIV-derived epitopes that exhibit diverse lengths and antigenicities (36). Strikingly, no immunodominant Gag-derived epitopes have been described (36). In contrast, many targeted epitopes emanate from the smaller regulatory/accessory proteins Nef and Vif (Table I) (37). Given the critical roles of these proteins with respect to infectivity and pathogenicity, such epitopes may be appealing targets for vaccine development.

CD8⁺ T cell responses restricted by Mamu-B*17 can be detected during both the acute and chronic phases of SIV infection (36), which suggests that this MHC I molecule could play important roles in the control of viral replication throughout the course of infection. However, the efficacy of immunodominant CD8⁺ T cell responses can be impaired by the selection of viral escape variants (38). Indeed, the emergence of escape mutations frequently correlates directly with the loss of viral suppression (38–40). Nevertheless, this phenomenon can impact viral fitness and reflects the potency of certain CD8⁺ T cell response (41). Many escape mutations within viral epitopes involve anchor residue substitutions that impede peptide binding to the corresponding MHC I molecule. In contrast, much of the observed sequence variation within Mamu-B*17–restricted epitopes does not seem to impair peptide–MHC I (pMHC I) binding substantially (42). Moreover, in the Mamu-B*17 setting, the C-terminal tryptophan anchor residues remain conserved, and amino acid substitutions only rarely affect the N-terminal anchors at positions 1, 2, or 3. Although variants of the HW8 epitope (Vif_66–73) can display substitutions in the N-terminal anchor residue, they maintain the ability to bind Mamu-B*17, which likely reflects amino acid compatibility and pocket B flexibility. Similarly, the Ile-to-Thr replacement at the N-terminal amino acid residue of the IW9 epitope (Nef_165–173) does not impact either Mamu-B*17 binding or CD8⁺ T cell recognition; rather, this mutation hinders Ag processing and/or presentation (42). Collectively, these features indicate that Mamu-B*17–restricted epitopes are favorable targets for effective CD8⁺ T cell immunity. Indeed, Mamu-B*17⁺ elite controllers (ECs) have been shown to resist rechallenge with variant SIV strains containing multiple escape mutations, and CD8⁺ T cell clones derived from ECs were more effective at suppressing viral replication than those derived from progressors (43).

The characteristics of peptide presentation by MHC I play a pivotal role in the antigenicity of an epitope (44–49). Accordingly, we determined the structures of eight SIV_mac239-derived epitopes in complex with Mamu-B*17 to define the atomic basis for effective epitope presentation by this protective MHC I molecule. Structural analysis revealed a novel peptide-binding strategy for the accommodation of diverse antigenic peptides, which informs our understanding of the association between Mamu-B*17 and the control of SIV replication.

The peptides used in this study (Table I) were synthesized at ∼90% purity as determined by HPLC reverse-phase chromatography (Scilight-Peptide). Peptides were stored in lyophilized aliquots at −80°C and dissolved in DMSO before use.

Mamu-B*17 H chain (extracellular domain, aa residues 1–276), human β₂-microglobulin (hβ2m), and rhesus macaque β₂-microglobulin (rβ2m) were expressed as inclusion bodies in Escherichia coli strain BL21 (DE3) and refolded with synthetically prepared SIV_mac239-derived peptides. Refolding was performed as described previously (50). Briefly, Mamu-B*17 H chain, β₂-microglobulin (β2m), and peptide were mixed at a molar ratio of 1:1:3 in refolding buffer (1 L comprising 100 mM Tris-HCl [pH 8], 400 mM L-Arg, 2 mM EDTA, 5 mM GSH, and 0.5 mM GSSG). After 24 h incubation at 4°C, the soluble portion of the refolded complex was concentrated and purified by gel filtration, followed by anion exchange chromatography and a second round of gel filtration, then finally concentrated to 10 mg/ml in 20 mM Tris-HCl (pH 8) and 50 mM NaCl for crystallization. The Mamu B*17 Vif_66–73 HW8 (HLEVQGYW) protein was refolded with hβ2m; all other complexes were refolded with rβ2m.

Protein concentrations were determined using a BCA protein assay according to the manufacturer’s instructions (Pierce). Crystal screens were initiated using commercial kits (Hampton Research). All crystallizations were performed using the hanging drop vapor diffusion technique. Plates were incubated at 291 K and examined after 72 h and 1 wk. Crystals of Mamu-B*17-HW8, Mamu-B*17-FW9, Mamu-B*17-MW9, and Mamu-B*17-GW10 were observed both in Index 44 (0.1 M HEPES [pH 7.5] and 25% w/v polyethylene glycol 3350) and Index 72 (0.2 M sodium chloride, 0.1 M HEPES [pH 7.5], and 25% w/v polyethylene glycol 3350). Crystals of Mamu-B*17-MF8, Mamu-B*17-IW9, and Mamu-B*17-IW11 were observed in Index 80 (0.2 M ammonium acetate, 0.1 M HEPES [pH 7.5], and 25% w/v polyethylene glycol 3350). Crystal of Mamu-B*17-QW9 were observed in Index 68 (0.2 M ammonium sulfate, 0.1 M HEPES [pH 7.5], and 25% w/v polyethylene glycol 3350). All crystals were soaked in reservoir solution supplemented with 20% glycerol as a cryoprotectant, then flash-cooled and maintained at 100 K in a cryostream. Data collection was performed in-house on a Rigaku R-AXIS IV++ image plate with a Rigaku MicroMax007 rotating-anode x-ray generator (Rigaku) operated at 40 kV and 20 mA (Cu Kα; λ = 1.5418 Å). Data were processed and scaled using HKL2000 (51).

The Mamu-B*17-HW8 structure was solved by the molecular replacement method using the HLA-B*5703 molecule (Protein Data Bank code 2BVO) as the search model with the program package Mosflm (52) and scaled with the program SCALA of the CCP4 program suite (53). The other datasets were determined by molecular replacement using the solved Mamu-B*17-HW8 structure as the search model with MOLREP (54). Extensive model building was performed by hand with COOT (55), and restrained refinement was performed using REFMAC5. Additional rounds of refinement were performed using the PHENIX package (56). The final structures displayed good stereochemistry (Table II), as assessed by the program PROCHECK (57), comprising residues 1–276 of the H chain and residues 1–99 of β2m. Structural figures were prepared with PyMOL. Solvent accessible surface areas were calculated with AreaMol in CCP4.

The atomic coordinates and the structure factors for all complexes in this study have been deposited in the Protein Data Bank with the following accession numbers: Mamu-B*17-IW9, 3RWC (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwc); Mamu-B*17-IW11, 3RWD (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwd); Mamu-B*17-FW9, 3RWE (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwe); Mamu-B*17-QW9, 3RWF (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwf); Mamu-B*17-MW9, 3RWG (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwg); Mamu-B*17-MF8, 3RWH (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwh); Mamu-B*17-GW10, 3RWI (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwi); and Mamu-B*17-HW8, 3RWJ (http://www.pdb.org/pdb/search/structidSearch.do?structureId=3rwj).

The structures of Mamu-B*17 complexed with eight different immunogenic SIV-derived peptides were determined in this study (Table I). X-ray data collection statistics are summarized in Table II. As expected, the overall domain arrangements and topologies of these Mamu-B*17 structures are similar to those of other mammalian MHC I molecules. The extracellular region of the Mamu-B*17 H chain forms a bedlike shape containing three domains (α1, α2, and α3). Specifically, the bedrail is composed of antiparallel α1 and α2 helices, which are supported by an eight-stranded β-sheet bedplate. The bound antigenic peptide lies along the bedrail. The α3 domain and β2m occupy the standard positions below the bedplate (Fig. 1). Both Mamu-B*17 and HLA-B*57 are enriched in EC cohorts and associated with the control of SIV and HIV replication, respectively. Amino acid sequence alignments (Fig. 2) reveal that Mamu-B*17 is quite similar to HLA-B*57, displaying 85.14% identity with HLA-B*5703. Moreover, the overall three-dimensional structure of Mamu-B*17 is similar to that of HLA-B*5703, with a root mean square difference of 0.709 Å.

Superposition of all eight peptides revealed the structural basis for length heterogeneity within Mamu-B*17–restricted epitopes (Fig. 3A). The majority of bound peptides adopt similar conformations with the P2 and C-terminal (Pc) residues serving as anchors, consistent with other pMHC I structures (Fig. 3A). Exceptions to this rule are HW8 and GW10. For HW8, His1 occupies pocket B to serve as the N-terminal anchor residue. For GW10, the two small amino acids Gly¹ and Ser² at the N terminus occupy pocket A, which results in P3 serving as an anchor residue. In accordance with previous studies, the primary anchor specificity at the C terminus was found to be associated with aromatic residues (W and F), which is similar to the situation for HLA-B*57–restricted peptides. Conversely, the N-terminal anchor residues for Mamu-B*17 appear to have a broad chemical specificity (R, H, T, Q) due to the adjustment of pocket B (discussed below). In addition, the secondary anchor residues (P_c-2 or P_c-3) also display diverse conformations (Fig. 3A).

Two comparisons are noteworthy (58, 59). First, compared with HW8, GW10 has two more N-terminal residues (Gly¹ and Ser²). However, the conformations of the central regions of the two peptides are essentially identical. Moreover, the solvent-accessible surface area for the central regions of HW8 (P3–P7) and GW10 (P5–P9) is similar (HW8 230 Ų, GW10 261.1 Ų) (Fig. 3B). In contrast, IW9 and IW11 present distinct conformations in the central region, although they share the first nine amino acids from their N termini. Specifically, IW11 contains two extra amino acids at the C terminus (Leu¹⁰ and Trp¹¹), which induce a switch in the usage of the Pc anchor residue from Trp⁹ in IW9 to Trp¹¹ in IW11 (Fig. 3C). This Pc anchor switch causes the central region (P4–P10) of IW11 to protrude out of the groove and into the solvent, with the main chain of IW11 shifting up to 7.6 Å higher than the equivalent regions of IW9. Furthermore, the solvent-accessible surface area of the central region of IW9 (P4–P8, 161.1Ų) shows a significant difference compared with IW11 (P4–P10, 410.7 Ų), which suggests that they might elicit qualitatively different TCR repertoires. Strikingly, a similar result has been reported for HLA-B*5703 (60). Thus, our structures show two distinct strategies used by MHC Ι molecules to present N- or C-terminal truncated peptides, which may partially reflect the intrinsic characteristics of the peptides themselves. An alternative molecular model of GW10 in complex with Mamu-B*17 was produced using COOT and CCP4, in which the peptide uses Ser² as the P2 anchor, and Gly¹ hides in pocket A instead of protruding out of the peptide binding groove (Fig. 4). Compared to the real Mamu-B*17-GW10 structure, however, we found that the interaction (van der Waal force and hydrogen bonds) between Ser² and pocket B in the alternative model was much weaker than the interaction between His³ and pocket B in the real Mamu-B*17-GW10 structure. Thus, GW10 adopts a proper conformation with the lowest Gibb’s free energy, which is similar to the situation for HW8.

The four nonameric peptides (IW9, FW9, QW9, and MW9) and one decameric peptide (GW10), which protrudes the additional P1 residue out of the groove, were compared in further analyses. As noted above, the second amino acid of GW10 is the small residue Ser, which is buried in pocket A. Thus, in this case, P3–P10 of GW10 is equivalent to P2–P9 of the nonameric peptides. Analysis of these five structures revealed that the conformation of nonamers presented by Mamu-B*17 can be divided into two types according to the binding mode in pocket D (Fig. 5). Type I is common in mammalian MHC I molecules. In this mode, the P3 residue (referring to P2 as the anchor residue) occupies the D pocket, stacking against the side chain of Tyrα¹⁵⁹. Both Mamu-B*17-IW9 and Mamu-B*17-FW9, which contain bulky aromatic residues at P3 (Tyr³ in IW9 and Trp³ in FW9) that fit pocket D well, display this conformation. In type II, the P3 residues are relatively small, which contributes to the spaciousness of pocket D and allows the accommodation of side chains contributed by other peptide residues. Mamu-B*17-QW9, Mamu-B*17-MW9, and Mamu-B*17-GW10 all fall into this category. Trp⁵ in QW9, Gln⁵ in MW9, and Val⁶ in GW10 occupy pocket D, respectively, due to the small side chains of the corresponding P3 residues (Ser³ in QW9, Pro³ in MW9, and Leu⁴ in GW10), which results in distinct main chain conformations relative to type I. Furthermore, compared with pocket D in Mamu-A*01 (accessible surface area 235.7Ų), which is optimal for binding the P3 proline side chain (50), pocket D in Mamu-B*17 is unusually large (average accessible surface area 321.4 Ų), thereby facilitating the formation of these distinct binding modes.

Previous studies have reported that water molecules (60–62), platform adjustment (60), or the presence of only one flexible pocket contribute to the accommodation variability of bound peptides. However, none of these binding modes involve flexibility of the whole groove. Further analysis of the Mamu-B*17 structures indicated that the side chains of residues on both the α1/α2 helices and the β-sheet can adopt different conformations, which confer important flexibility to the peptide-binding groove for the accommodation of different peptide conformations (Fig. 6A).

Gluα⁴⁵, Argα⁶⁶, Gluα⁶⁹, and Hisα⁷⁴ located on the α1 helix are all involved in interactions with bound peptides. Furthermore, the side chains of these four residues present various conformations to accommodate different peptides. For example, in the Mamu-B*17-IW9 and Mamu-B*17-GW10 structures, the side chains of Gluα⁶⁹ extend in distinct directions as a consequence of the different P6 residues (corresponding to P7 in GW10) in these two peptides. Specifically, for IW9, the side chain of Thr⁶ hydrogen bonds to the OE1 atom of Gluα⁶⁹, which forces the side chain of Gluα⁶⁹ to orientate toward the peptide. In contrast, for GW10, the side chain of Gln⁷ shifts 2.37 Å to form hydrogen bonds with the OE1/OE2 atoms of Gluα⁶⁹, causing the side chain of Gluα⁶⁹ to protrude up out of the groove (Fig. 6B).

In contrast to the central location of flexible residues in the α1 helix, the flexible residues in the α2 helix that are involved in peptide binding are distributed from the N terminus to the C terminus. The structures of Mamu-B*17-QW9 and Mamu-B*17-MW9 reveal conformational shifts in the side chains of Argα¹⁵⁵ and Asnα¹⁵⁰ (Fig. 6C). For Mamu-B*17-QW9, two salt bridges are formed between the basic Argα¹⁵⁵ guanidinium head group and the OD1/OD2 oxygen atoms of the QW9 acidic Asp⁷, respectively. For Mamu-B*17-MW9, the side chain of Argα¹⁵⁵ is much closer to the α2-helix due to hydrogen bonds with Asnα¹⁵⁰. The side chain of Asnα¹⁵⁰ is orientated toward the peptide and contributes to the stabilization of the side chain of peptide residue Ser⁷ by forming a hydrogen bond between the ND2 atom and the oxygen atom of Ser⁷.

Superposing whole residues comprising the peptide binding groove in the Mamu-B*17-IW9 and Mamu-B*17-IW11 structures revealed that Tyrα¹⁵² in the α2-helix of the H chain also contributes to different peptide accommodation modes (Fig. 6D). Indeed, the side chain extends in totally different directions as a result of interactions with different peptide residues. Specifically, in case of the IW11 peptide, the side chain of Trp⁹ is orientated toward the bottom of the peptide-binding groove, which forms a hydrogen bond to Lysα⁹⁷. The side chain of Tyrα¹⁵² pokes toward the N terminus of the peptide, and the hydroxyl group hydrogen bonds to the side chains of Lysα⁹⁷ and Hisα¹¹⁴, respectively. In contrast, the side chain of Phe⁷ in IW9 is directed toward the α2-helix and occupies pocket E, which forces the phenolic group of Tyrα¹⁵² to swivel away and leave enough space to accommodate the aromatic side chain.

In the structures of Mamu-B*17 complexed with different peptides, H chain position 97 is located at the bottom of the peptide-binding groove as for other classical MHC I molecules. The conformational plasticity of Lysα⁹⁷ contributes to the accommodation of different peptide residues that insert into the central region of the groove accordingly. For example, in the Mamu-B*17-FW9 structure, the Lysα⁹⁷ side chain helps to stabilize the side chain of Glu⁷ by forming a salt bridge. In the Mamu-B*17-MF8 structure, however, the side chain of Lysα⁹⁷ shifts 3.25Å to leave enough space for the hydrophobic side chain of Leu⁵ (Fig. 6E).

In most mammalian MHC I molecules, the peptide-binding motif generally specifies two or more positions (anchor positions) at which all suitable peptides have either one or a very limited set of permissible residues (63, 64). Strikingly, pocket B of Mamu-B*17 can bind a wide range of anchor residues. In accordance with previous data (36), the small residue T, the bulky residues R and H, and the bulky polar aliphatic residue Q, can all be accommodated in pocket B. On one hand, pocket B of Mamu-B*17 is much deeper compared with that of Mamu-A*01 and Mamu-A*02 (Fig. 7A). Sequence analysis reveals that position 63 and position 67 in Mamu-A*01 and Mamu-A*02 are glutamine and methionine, respectively (Fig. 2), the side chains of which are much longer than their counterparts in Mamu-B*17, thereby resulting in a relatively shallow pocket B. In contrast, the small alanine side chains in both positions 63 and 67 contribute to the spaciousness of pocket B in Mamu-B*17, enabling the accommodation of bulky anchor residues (Fig. 7A). On the other hand, the unique charged Gluα⁴⁵, which is located at the bottom of pocket B, also plays an important role in the binding of various peptide anchor residues (Fig. 7B). For IW9, the side chain of Gluα⁴⁵ engages in two of the four hydrogen bonds that are formed by the guanidinium moiety of peptide Arg², the other two being formed with Tyrα⁹ and Serα²⁴. For QW9, the side chain of Gluα⁴⁵ rotates to connect to the short side chain of peptide Thr² via a water molecule, which is stabilized by Alaα⁶³ located on the α1-helix. The side chains lengths of peptide Gln² in FW9 and peptide His³ in GW10 are similar and adopt a similar conformational orientation with respect to Gluα⁴⁵ and Tyrα⁹, although the interaction between peptide Gln² and Gluα⁴⁵ is a little bit weaker than that between peptide His³ and Gluα⁴⁵. Furthermore, the charged residues Argα⁶⁶ and Gluα¹⁶³ form a salt bridge above pocket B, which forces anchor residues to insert deeply into this pocket.

The large volume of Mamu-B*17 pocket F is composed of hydrophobic amino acids (Ileα⁹⁵, Tyrα¹²³, and Tyrα¹¹⁸), which makes it suitable for binding large aromatic C-terminal side chains (W and F). Notably, Alaα⁸¹ at the bottom of pocket F plays an important role in the accommodation of large aromatic anchors, although it does not generate many contacts with the anchor residues. Compared with Leuα⁸¹ in Mamu-A*01, the small side chain of Alaα⁸¹ in Mamu-B*17 provides pocket F with sufficient volume to accommodate large aromatic anchors. Thus, pocket F of Mamu*17 can accommodate large aromatic anchors, whereas pocket F of Mamu-A*01 can only bind to relatively small side chain residues. The C-terminal binding motif of Mamu-B*17–restricted peptides is similar to that for HLA-B*57–restricted peptides. Serα¹¹⁶ and Ileα⁹⁵ in Mamu-B*17 also contribute to the shape of pocket F; these residues are conserved in HLA-B*5701. Although tyrosine occupies position 116 in HLA-B*5703 (Fig. 2), the side chain is orientated toward the central region of the groove, allowing similar F-anchor preference.

Previous studies have indicated that key residues on the α1 and α2 helices, including residues 65–76 and residues 149–156, play an important role in mediating pMHC I interactions with the TCR (65–67). Notably, these residues in Mamu-B*17 present highly flexible conformations, which may influence TCR repertoire profiles (Fig. 8). Position 69 and position 155 have been reported as crucial residues for TCR interactions (67). Sequence analysis reveals that Gluα⁶⁹ and Argα¹⁵⁵ in Mamu-B*17 are unique (Fig. 2), as the corresponding residues in other primate MHC I molecules are noncharged (S and Q). These unique features may contribute to a more flexible juxtaposition at the TCR–pMHC I interface, with potential implications for TCR repertoire engagement.

The Mamu-B*17 allele is prevalent among rhesus macaques and consistently associated with efficacious control of SIV replication. In this article, we describe the structures of eight different immunodominant SIV_mac239-derived CTL-epitope peptides complexed with Mamu-B*17, thereby providing the first insights into the atomic basis of Ag presentation by this protective MHC I molecule.

The peptide-binding specificity of Mamu-B*17 has been characterized previously in functional studies (36). Pocket B and pocket F are clearly the dominant peptide anchor sites, as observed for other MHC I complexes. N-terminal peptide anchor residues display a broad chemical specificity, encompassing basic residues (H and R), a bulky polar aliphatic residue (Q), and a small residue (T). This diverse profile is determined by two main structural features of the Mamu-B*17 molecule. First, pocket B of Mamu-B*17 is much deeper and larger than that of either Mamu-A*01 or Mamu-A*02 (50, 68), which provides more space for bulky residues. In contrast, pocket B of Mamu-A*01 can only accommodate small residues (S and T) (50). Second, the conformational adjustment of side chains and water molecule compensation confer substantial plasticity within pocket B. Single substitution analog assays have shown that negatively charged residues (D and E) are not tolerated at position 2 (36), which may be partially explained by the Gluα⁴⁵ residue positioned at the bottom of pocket B. Pocket F in the Mamu-B*17 molecule is particularly distinctive in that it confers a preference for bulky aromatic residues, especially tryptophan, as the C terminus of the bound peptide. Many HLA-B*57 suballeles show similar C-terminal anchor residue preference due to the presence of identical key residues in this pocket (60). Previous studies have failed to detect the emergence of natural mutations that change the C terminus tryptophan anchor residue (69). Given that tryptophan is a rare amino acid, encoded only by one codon, these observations indicate that such variation would likely impact viral fitness and provide a rationale for the protective effect of Mamu-B*17–restricted epitope presentation.

The conformations of the eight peptide epitopes complexed to Mamu-B*17 described in this study are distinct, which suggests the potential to elicit a broad range of protective CD8⁺ T cell responses. In addition, many studies show that water molecules, platform adjustment, or the presence of only one flexible pocket contribute to the accommodation of different peptides (60–62). In contrast, Mamu-B*17 has a whole flexible peptide-binding groove to achieve this. Furthermore, Mamu-B*17 appears to maintain the ability to bind variant epitopes, which may elicit cross-reactive TCRs or specific de novo responses (43). It is tempting to speculate that the unique flexibility within the Mamu-B*17 binding groove may enable the accommodation of natural epitope variants, thereby providing a novel explanation for the containment of viral replication by this MHC I molecule.

TCR cross-reactivity (18, 70) or variant-specific de novo responses (71, 72) might be important for the maintenance of SIV control in ECs. Among the structures determined in this study, two sets of related peptides present distinct outcomes. The GW10 and HW8 peptides display identical main-chain and side-chain conformations, although GW10 contains two more amino acids (Gly¹ and Ser²) at the N terminus. Thus, HW8 and GW10 might elicit similar TCR repertoires. In contrast, IW9 and IW11 display distinct main-chain conformations across the central region. Specifically, IW11 extends two more amino acids (Leu¹⁰ and Trp¹¹) at the C terminus, inducing an anchor residue shift in pocket F. Consequently, the central region of IW11 bulges out of the groove, which likely plays a dominant role in TCR recognition. The identical main-chain conformations of the P1 to P4 and the Pc-1 to Pc-2 residues in IW9 and IW11 lock both the N terminus and C terminus, respectively. Two related epitopes, KF8 and KF11, show similarly distinct features when bound to HLA-B*5703 (60). The structures of Mamu-B*17 complexed with different peptides therefore provide insights into the relationship between different epitopes. However, extrapolations to TCR repertoire engagement remain untested and require further exploration.

In summary, the current study provides novel insights into the structural basis of diverse peptide accommodation by Mamu-B*17 and highlights unique atomic features that might contribute to the protective effect of this MHC I molecule in SIV infection.

We thank Drs. Yi Shi and Hao Cheng from the Institute of Microbiology, Chinese Academy of Sciences, for excellent suggestions regarding the study. We also thank Bernard Lafont for helpful discussions.

The authors have no financial conflicts of interest.