3BY1

Unliganded Norvalk Virus P domain

Summary for 3BY1

• Entry DOI: 10.2210/pdb3by1/pdb
• Related: 1IHM 3BY2 3BY3
• Descriptor: 58 kd capsid protein (2 entities in total)
• Functional Keywords: norwalk virus p domain, viral protein
• Biological source: Norwalk virus
• Cellular location: Virion: Q83884
• Total number of polymer chains: 1
• Total formula weight: 33497.65

Authors

Hegde, R.,Bu, W. (deposition date: 2008-01-15, release date: 2008-04-22, Last modification date: 2024-02-21)

Primary citation

Bu, W.,Mamedova, A.,Tan, M.,Xia, M.,Jiang, X.,Hegde, R.S.
Structural basis for the receptor binding specificity of Norwalk virus.
J.Virol., 82:5340-5347, 2008

PubMed Abstract: Noroviruses are positive-sense, single-stranded RNA viruses that cause acute gastroenteritis. They recognize human histo-blood group antigens as receptors in a strain-specific manner. The structures presented here were analyzed in order to elucidate the structural basis for differences in ligand recognition of noroviruses from different genogroups, the prototypic Norwalk virus (NV; GI-1) and VA387 (GII-4), which recognize the same A antigen but differ in that NV is unable to bind to the B antigen. Two forms of the receptor-binding domain of the norovirus coat protein, the P domain and the P polypeptide, that were previously shown to differ in receptor binding and P-particle formation properties were studied. Comparison of the structures of the NV P domain with and without A trisaccharide and the NV P polypeptide revealed no major ligand-induced changes. The 2.3-A cocrystal structure reveals that the A trisaccharide binds to the NV P domain through interactions with the residues Ser377, Asp327, His329, and Ser380 in a mode distinct from that previously reported for the VA387 P-domain-A-trisaccharide complex. Mutational analyses confirm the importance of these residues in NV P-particle binding to native A antigen. The alpha-GalNAc residue unique to the A trisaccharide is buried deeply in the NV binding pocket, unlike in the structures of A and B trisaccharides bound to VA387 P domain, where the alpha-fucose residue forms the most protein contacts. The A-trisaccharide binding mode seen in the NV P domain complex cannot be sterically accommodated in the VA387 P domain.

PubMed: 18385236
DOI: 10.1128/JVI.00135-08

Experimental method

X-RAY DIFFRACTION (2.69 Å)