Crystal structure of a superantigen bound to MHC class II displays zinc and peptide dependence

Abstract

The three-dimensional structure of a bacterial superantigen, Staphylococcus aureus enterotoxin H (SEH), bound to human major histocompatibility complex (MHC) class II (HLA-DR1) has been determined by X-ray crystallography to 2.6 A resolution (1HXY). The superantigen binds on top of HLA-DR1 in a completely different way from earlier co-crystallized superantigens from S.aureus. SEH interacts with high affinity through a zinc ion with the beta1 chain of HLA-DR1 and also with the peptide presented by HLA-DR1. The structure suggests that all superantigens interacting with MHC class II in a zinc-dependent manner present the superantigen in a common way. This suggests a new model for ternary complex formation with the T-cell receptor (TCR), in which a contact between the TCR and the MHC class II is unlikely.

Fig. 1. Gel filtration analyses of the HLA-DR1 complex, measuring the fluorescence. (A) SEH, (B) the HLA-DR1–peptide complex, (C) SEH and the HLA-DR1–peptide complex in the presence of zinc, and (D) SEH and the HLA-DR1–peptide complex in the presence of EDTA.

Fig. 2. Ribbon representation of the HLA-DR1–SEH complex with HLA-DR1 (green), HA-peptide (red) and SEH (yellow).

Fig. 3. Surface representation of HLA-DR1 (grey) with the residues involved in hydrogen bonding to SEH marked in green. The β-sheets on SEH (β6, β7, β9, β10 and β12) that are interacting with HLA-DR1 are drawn in yellow and the antigen peptide is in red. Side chains on SEH forming hydrogen bonds are coloured orange.

Fig. 4. The coordination and hydrogen bond pattern of selected residues in the region around the zinc ion (magenta) and the HA-peptide (grey)–HLA-DR1 (green)–SEH (yellow) complex. An additional hydrogen bond between Asp208s, OD1 and Asn113s, ND2 (2.7 Å) is observed but omitted in the picture for clarity.

Fig. 5. Electron density from the final 2.6 Å 2F_o – F_c map of the HA-peptide–SEH interaction, contoured at 1σ, with the HA-peptide (green) and SEH (yellow). Gln120s forms a bidentate hydrogen bond with Lys310p (p3).

Fig. 6. Sequence alignment of the zinc family of superantigens and SEB. Residues involved in the HLA-DR1–SEH interaction are marked in yellow. Numbering is according to SEH. The N-terminal parts of the sequences are not shown.

Fig. 7. Comparison between the HLA-DR2a–MBP peptide–SPE-C complex (Li et al., 2001, 1HQR) and the HLA-DR1–HA-peptide–SEH complex. The superposition was made by fitting the α-chains of the HLA-DRs to each other. The MBP peptide is marked in cyan, the HA-peptide in red, SEH in yellow and SPE-C in blue. The β-chain of HLA-DR1 is represented as a surface (grey).