3ASR

Crystal structure of P domain from Norovirus Funabashi258 stain in the complex with Lewis-a

3ASR の概要

• エントリーDOI: 10.2210/pdb3asr/pdb
• 関連するPDBエントリー: 3ASP 3ASQ 3ASS 3AST
• 関連するBIRD辞書のPRD_ID: PRD_900129
• 分子名称: Capsid protein, beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose, SODIUM ION, ... (5 entities in total)
• 機能のキーワード: protein-sugar complex, histo-blood group antigen, capsid protein, lectin-like protein, viral protein
• 由来する生物種: Norwalk-like virus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 71763.35

構造登録者

Kubota, T.,Kumagai, A.,Itoh, H.,Furukawa, S.,Narimatsu, H.,Wakita, T.,Ishii, K.,Takeda, N.,Someya, Y.,Shirato, H. (登録日: 2010-12-17, 公開日: 2012-01-25, 最終更新日: 2023-11-01)

主引用文献

Kubota, T.,Kumagai, A.,Ito, H.,Furukawa, S.,Someya, Y.,Takeda, N.,Ishii, K.,Wakita, T.,Narimatsu, H.,Shirato, H.
Structural basis for the recognition of Lewis antigens by genogroup I norovirus
J.Virol., 86:11138-11150, 2012

PubMed Abstract: Noroviruses (NoVs) bind to histo-blood group antigens, namely, ABH antigens and Lewis antigens. We previously showed the NoVs GI/2, GI/3, GI/4, and GI/8 were able to strongly bind to Lewis a (Le(a)) antigen, which is expressed by individuals who are nonsecretors. In this study, to investigate how Lewis antigens interact with GI NoV virion protein 1 (VP1), we determined the crystal structures of the P domain of the VP1 protein from the Funabashi 258 (FUV258) strain (GI/2) in complexes with Le(a), Le(b), H type 1, or A type 1 antigens. The structures were compared with those of the NV/68 strain (GI/1), which does not bind to the Le(a) antigen. The four loop structures, loop P, loop S, loop A, and loop B, continuously deviated by more than 2 Å in length between the Cα atoms of the corresponding residues of the FUV258 and NV/68 P domains. The most pronounced differences between the two VP1 proteins were observed in the structures of loop P. In the FUV258 P domain, loop P protruded toward the next protomer, forming a Le(a) antigen-binding site. The Gln389 residue make a significant contribution to the binding of the Le(a) antigen through the stabilization of loop P as well as through direct interactions with the α4-fucosyl residue (α4Fuc) of the Le(a) antigen. Mutation of the Gln389 residue dramatically affected the degree of binding of the Lewis antigens. Collectively, these results suggest that loop P and the amino acid residue at position 389 affect Lewis antigen binding.

PubMed: 22855491
DOI: 10.1128/JVI.00278-12

実験手法

X-RAY DIFFRACTION (1.6 Å)