3R6J

Crystal Structure of the Capsid P Domain from Norwalk Virus Strain Hiroshima/1999

Summary for 3R6J

• Entry DOI: 10.2210/pdb3r6j/pdb
• Related: 3ONU 3ONY 3PA1 3PA2 3Q38 3Q39 3Q3A 3Q6Q 3Q6R 3R6K
• Descriptor: VP1 protein, 1,2-ETHANEDIOL (3 entities in total)
• Functional Keywords: norovirus, p-domain, capsid, receptor, histo blood group antigen (hbga), viral protein
• Biological source: Norwalk-like virus
• Total number of polymer chains: 1
• Total formula weight: 33476.57

Authors

Hansman, G.S.,Biertumpfel, C.,McLellan, J.S.,Georgiev, I.,Chen, L.,Zhou, T.,Katayama, K.,Kwong, P.D. (deposition date: 2011-03-21, release date: 2011-05-11, Last modification date: 2023-09-13)

Primary citation

Hansman, G.S.,Biertumpfel, C.,Georgiev, I.,McLellan, J.S.,Chen, L.,Zhou, T.,Katayama, K.,Kwong, P.D.
Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability.
J.Virol., 85:6687-6701, 2011

PubMed Abstract: Noroviruses are the dominant cause of outbreaks of gastroenteritis worldwide, and interactions with human histo-blood group antigens (HBGAs) are thought to play a critical role in their entry mechanism. Structures of noroviruses from genogroups GI and GII in complex with HBGAs, however, reveal different modes of interaction. To gain insight into norovirus recognition of HBGAs, we determined crystal structures of norovirus protruding domains from two rarely detected GII genotypes, GII.10 and GII.12, alone and in complex with a panel of HBGAs, and analyzed structure-function implications related to conservation of the HBGA binding pocket. The GII.10- and GII.12-apo structures as well as the previously solved GII.4-apo structure resembled each other more closely than the GI.1-derived structure, and all three GII structures showed similar modes of HBGA recognition. The primary GII norovirus-HBGA interaction involved six hydrogen bonds between a terminal αfucose1-2 of the HBGAs and a dimeric capsid interface, which was composed of elements from two protruding subdomains. Norovirus interactions with other saccharide units of the HBGAs were variable and involved fewer hydrogen bonds. Sequence analysis revealed a site of GII norovirus sequence conservation to reside under the critical αfucose1-2 and to be one of the few patches of conserved residues on the outer virion-capsid surface. The site was smaller than that involved in full HBGA recognition, a consequence of variable recognition of peripheral saccharides. Despite this evasion tactic, the HBGA site of viral vulnerability may provide a viable target for small molecule- and antibody-mediated neutralization of GII norovirus.

PubMed: 21525337
DOI: 10.1128/JVI.00246-11

Experimental method

X-RAY DIFFRACTION (1.75 Å)