All of these toxins share a similar two-domain fold (N and C-terminal domains) with a long alpha-helix in the middle of the molecule, a characteristic beta-barrel known as the "oligosaccharide/oligonucleotide fold" at the N-terminal domain and a beta-grasp motif at the C-terminal domain. Each superantigen possesses slightly different binding mode(s) when it interacts with MHC class II molecules or the T-cell receptor.
The N-terminal domain is also referred to as OB-fold, or in other words the oligonuclucleotide binding fold. This region contains a low-affinity major histocompatibility complex class II (MHC II) site which causes an inflammatory response.
The N-terminal domain contains regions involved in Major Histocompatibility Complex class II association. It is a five stranded beta barrel that forms an OB fold.
The beta-grasp domain has some structural similarities to the beta-grasp motif present in immunoglobulin-binding domains, ubiquitin, 2Fe-2 S ferredoxin and translation initiation factor 3 as identified by the SCOP database.
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