8ybn | pdb_00008ybn

Crystal structure of nanobody SEB-Nb8 bound to staphylococcal enterotoxin B (SEB)

spinqualitylabelsall models 8ybn, resolution 2.18Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 8ybn is a 2 chain structure with sequence from Staphylococcus aureus and Vicugna pacos. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.18Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function ETXB_STAAU Staphylococcal enterotoxins cause the intoxication staphylococcal food poisoning syndrome. The illness characterized by high fever, hypotension, diarrhea, shock, and in some cases death. Publication Abstract from PubMed Staphylococcal Enterotoxin Type B (SEB), produced by Staphylococcus aureus bacteria, is notorious for inducing severe food poisoning and toxic shock syndrome. While nanobody-based treatments hold promises for combating SEB-induced diseases, the lack of structural information between SEB and nanobodies has hindered the development of nanobody-based therapeutics. Here, we present crystal structures of SEB-Nb3, SEB-Nb6, SEB-Nb8, SEB-Nb11, and SEB-Nb20 at resolutions ranging from 1.59 A to 2.33 A. Crystallographic analysis revealed that Nb3, Nb8, Nb11, and Nb20 bind to SEB at the T-cell receptor (TCR) interface, while Nb6 binds at the major histocompatibility complex (MHC) interface, suggesting their potential to inhibit SEB function by disrupting interactions with TCR or MHC molecules. Molecular biological analyses confirmed the thermodynamic and kinetic parameters of Nb3, Nb5, Nb6, Nb8, Nb11, Nb15, Nb18, and Nb20 to SEB. The competitive inhibition was further confirmed by cell-based experiments demonstrating nanobody neutralization. These findings elucidate the structural basis for developing specific nanobodies to neutralize SEB threats, providing crucial insights into the underlying mechanisms and offering significant assistance for further optimization towards future therapeutic strategies. Structural insights into the binding of nanobodies to the Staphylococcal enterotoxin B.,Zong X, Liu P, Wang Z, Zhu H, Zhong C, Zhong P, Jiang H, Liu J, Ma Z, Liu X, Liu R, Ding Y Int J Biol Macromol. 2024 Sep;276(Pt 2):133957. doi: , 10.1016/j.ijbiomac.2024.133957. Epub 2024 Jul 17. PMID:39029852 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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