3ASR

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

Summary for 3ASR

• Entry DOI: 10.2210/pdb3asr/pdb
• Related: 3ASP 3ASQ 3ASS 3AST
• Related PRD ID: PRD_900129
• Descriptor: 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)
• Functional Keywords: protein-sugar complex, histo-blood group antigen, capsid protein, lectin-like protein, viral protein
• Biological source: Norwalk-like virus
• Total number of polymer chains: 2
• Total formula weight: 71763.35

Authors

Kubota, T.,Kumagai, A.,Itoh, H.,Furukawa, S.,Narimatsu, H.,Wakita, T.,Ishii, K.,Takeda, N.,Someya, Y.,Shirato, H. (deposition date: 2010-12-17, release date: 2012-01-25, Last modification date: 2023-11-01)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.6 Å)