Crystal structure of staphylococcal enterotoxin I (SEI) in complex with a human major histocompatibility complex class II molecule

Abstract

Superantigens are bacterial or viral proteins that elicit massive T cell activation through simultaneous binding to major histocompatibility complex (MHC) class II and T cell receptors. This activation results in uncontrolled release of inflammatory cytokines, causing toxic shock. A remarkable property of superantigens, which distinguishes them from T cell receptors, is their ability to interact with multiple MHC class II alleles independently of MHC-bound peptide. Previous crystallographic studies have shown that staphylococcal and streptococcal superantigens belonging to the zinc family bind to a high affinity site on the class II beta-chain. However, the basis for promiscuous MHC recognition by zinc-dependent superantigens is not obvious, because the beta-chain is polymorphic and the MHC-bound peptide forms part of the binding interface. To understand how zinc-dependent superantigens recognize MHC, we determined the crystal structure, at 2.0 A resolution, of staphylococcal enterotoxin I bound to the human class II molecule HLA-DR1 bearing a peptide from influenza hemagglutinin. Interactions between the superantigen and DR1 beta-chain are mediated by a zinc ion, and 22% of the buried surface of peptide.MHC is contributed by the peptide. Comparison of the staphylococcal enterotoxin I.peptide.DR1 structure with ones determined previously revealed that zinc-dependent superantigens achieve promiscuous binding to MHC by targeting conservatively substituted residues of the polymorphic beta-chain. Additionally, these superantigens circumvent peptide specificity by engaging MHC-bound peptides at their conformationally conserved N-terminal regions while minimizing sequence-specific interactions with peptide residues to enhance cross-reactivity.

FIGURE 1. Structure of the SEI·HA·HLA-DR1 complex

A, ribbon diagram of the SEI·HA·HLA-DR1 complex showing the overall structure. The HLA-DR1 α-chain is green, and the β-chain is blue; SEI is yellow; peptide is pink. The interface zinc ion is drawn as a red sphere. B, detailed view (stereo diagram) of the interface between SEI and HA·HLA-DR1. Color codes are the same as in A. Residues of SEI (yellow) in contact with residues of the HLA-DR1 β-chain (green) and the HA peptide (purple) are drawn. Hydrogen bonds are represented as dashed lines. The bridging zinc ion is tetrahedrally coordinated by SEI residues His¹⁶⁹, His²⁰⁷, and Asp²⁰⁹ and by HLA-DR1 residue His^81β.

FIGURE 2. Structure of the β4-β5 loop of SEI

A, electron density from the final 2F_o − F_c map at 2.0 Å resolution showing SEI residues 70–75 in a stick representation. Carbon atoms are green, nitrogen atoms are blue, oxygen atoms are red, and the sulfur atom is yellow. B, superposition of SEI (cyan) onto SPEC (red) in the SPEC·Vβ2.1 structure (38). Steric clashes are observed between the β4-β5 loop of SEI (blue) and CDR1 (yellow) and CDR2 (brown) of Vβ2.1. CDR3 is purple; hypervariable region 4 (HV4) and framework region 3 (FR3) are green. The β4-β5 loop of SPEC is pink.

FIGURE 3. Structure-based sequence alignment of the zinc family of superantigens

Secondary structure elements for SEI (top) are denoted by squiggles (α-helices and 3₁₀ helices (η)) and arrows (β-strands); these are numbered according to their order of appearance in the sequences. Numbers at the top refer to SEI residues. White characters on a red background show strictly conserved residues. Residues that are well conserved are drawn in red and framed in blue. The remaining residues are black. Triangles above the SEI sequence mark residues involved in interactions with HA·HLA-DR1 in the crystal structure. The three residues involved in Zn²⁺ coordination in SEI are marked with green triangles; other interacting residues are marked with blue triangles. Sequence alignments were performed with ClustalW, and the figure was generated using ESPript.

FIGURE 4. Interactions in the SEI·HA·DR1, SEH·HA·DR1, and SPEC·MBP·DR2a interfaces

A, interactions between the HLA-DR1 β3-chain (blue) and SEI (yellow) in the SEI·HA·DR1 complex. The DR1 α-chain (green) does not contact SEI. Residues of the DR1 β-chain involved in interactions with SEI are green. The interface zinc ion is drawn as a red sphere. Hydrogen bonds are represented as dashed lines. Oxygen and nitrogen atoms are colored red and blue, respectively. B, interactions between the HA peptide (pink) and SEI (yellow). Peptide residues P–1 Lys and P2 Val (purple) contact the SAG. C, Zn²⁺ coordination in the SEI·HA·DR1 complex. The zinc ion is tetrahedrally coordinated by SEI residues His¹⁶⁹, His²⁰⁷, and Asp²⁰⁹ (yellow) and by HLA-DR1 residue His^81β (green). D, interactions between the HLA-DR1 β-chain (blue) and SEH (yellow) in the SEH·HA·DR1 complex. Residues Asp-55α and Asn^57α of the DR1 α-chain (green) also contact SEH. E, interactions between the HA peptide (pink) and SEH (yellow). Peptide residues P–1 Lys and P3 Lys (purple) contact the SAG. F, Zn²⁺ coordination in the SEH·HA·DR1 complex. The zinc ion is coordinated by SEH residues His²⁰⁶ and Asp²⁰⁸ (yellow) and by DR1 residue His^81β (green). G, interactions between the HLA-DR2a β-chain (blue) and SPEC (yellow) in the SPEC·MBP·DR2a complex. The DR2a α-chain (green) does not contact SPEC. H, interactions between the MBP peptide (pink) and SPEC (yellow). Peptide residues P–3 Val, P–2 His, P–1 Phe, P2 Lys, and P3 Asn (purple) contact the SAG. I, Zn²⁺ coordination in the SPEC·MBP·DR2a complex. The zinc ion is coordinated tetrahedrally by SPEC residues His¹⁶⁷, His²⁰¹, and Asp²⁰³ (yellow) and by HLA-DR2a residue His^81β (green).