Large motions the protruding domain in a native iflavirus

Sergei Kalynych1, Antonin Přidal2, Yevhen Levdansky1, Lenka Palkova, Joachim de Miranda3, and Pavel Plevka1,*

1Structural Virology Group, Central European Institute of Technology, Masaryk University, Kamenice 753/35, Brno, Czech Republic, 625 00;

2Faculty of Agronomy, Mendel’s University, Zemedelska 1,Brno, Czech Republic, 613 00;

3Swedish University of Agricultural Sciences, Department of Ecology, Uppsala, Sweden, 750 07

Iflaviruses are non-enveloped single-stranded RNA viruses, which infect various insects including economically important agricultural pollinators honeybees and bumblebees. Studies of the life cycle and pathogenesis of iflaviruses are impeded by the lack of a honeybee cell cultures. Here, we present two crystal structures of an iflavirus Slow Bee Paralysis Virus (SBPV) purified from a natural source, solved at 3.4 Å and 2.6 Å resolutions. We found that the C-terminus of a capsid protein VP3 forms a protruding domain (P-domain) located on the virion surface. The P-domain exhibits a novel fold, which is different from that seen in any other viruses characterized to date. P-domains undergo large movements toward icosahedral five-fold axis, where they are found in a crown-like arrangement. Despite sharing the same quasi T=3 symmetry with known insect picorna-like viruses, SBPV exhibits a unique surface topology and differs in the overall organization of the capsid. Our findings provide structural framework for further investigations of infection mechanisms employed by the agriculturally important class of viral pathogens.