The three-dimensional structure of ryegrass mottle virus at 2.9 Å resolution

Pavel Plevka¹, Kaspars Tars¹, Erkki Truve², Ina Balke³, Andris Zeltins³, Lars Liljas¹

¹ Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden

² Department of Gene Technology, Tallinn University of Technology, Akademia tee 15, 19086 Tallinn, Estonia.

³ Biomedical Research and Study Centre, Ratsupites 1, LV 1067, Riga, Latvia

The crystal structure of ryegrass mottle virus (RGMV) has been determined at 2.9Å resolution. The icosahedral capsid contains 180 copies of the coat protein arranged with T=3 quasi-symmetry. The coat protein has a jellyroll β-sandwich fold similar to the other sobemoviruses. A comparison of the sequences and structures of viruses in the genus shows that the RGMV coat protein has a deletion in one of the loop regions that are conserved among the other sobemoviruses. The full-size loop contains a helix that participates in the stabilization of the N-terminal arms. The structure of RGMV appears to compensate for the deletion by having longer β-strands in the N-terminal arm. The interactions of coat proteins within the icosahedral asymmetric unit of sobemoviruses usually involve calcium ions. We could not identify any density for metal ions in the proximity of the conserved residues normally involved in calcium binding. Nevertheless, calcium ions are necessary for RGMV particle stability at neutral pH, since particles depleted of calcium disassemble at high ionic strength. A likely reason for the absence of the calcium ion is the low pH of the crystallization buffer.

Keywords: Ryegrass mottle virus; Sobemovirus; Virus structure; Virus assembly