2IZW

Crystal structure of Ryegrass Mottle Virus

Summary for 2IZW

• Entry DOI: 10.2210/pdb2izw/pdb
• Descriptor: RYEGRASS MOTTLE VIRUS COAT PROTEIN (1 entity in total)
• Functional Keywords: rna, virus, assembly, capsid protein
• Biological source: RYEGRASS MOTTLE VIRUS
• Total number of polymer chains: 3
• Total formula weight: 76571.65

Authors

Plevka, P.,Tars, K.,Zeltins, A.,Balke, I.,Truve, E.,Liljas, L. (deposition date: 2006-07-27, release date: 2007-10-02, Last modification date: 2023-12-13)

Primary citation

Plevka, P.,Tars, K.,Zeltins, A.,Balke, I.,Truve, E.,Liljas, L.
The Three-Dimensional Structure of Ryegrass Mottle Virus at 2.9 A Resolution.
Virology, 369:364-, 2007

PubMed Abstract: The crystal structure of the sobemovirus Ryegrass mottle virus (RGMoV) has been determined at 2.9 A resolution. The coat protein has a canonical jellyroll beta-sandwich fold. In comparison to other sobemoviruses the RGMoV coat protein is missing several residues in two of the loop regions. The first loop contributes to contacts between subunits around the quasi-threefold symmetry axis. The altered contact interface results in tilting of the subunits towards the quasi-threefold axis. The assembly of the T=3 capsid of sobemoviruses is controlled by the N-termini of C subunits forming a so-called beta-annulus. The other loop that is smaller in the RGMoV structure contains a helix that participates in stabilization of the beta-annulus in other sobemoviruses. The loss of interaction between the RGMoV loop and the beta-annulus has been compensated for by additional interactions between the N-terminal arms. As a consequence of these differences, the diameter of the RGMoV particle is 8 A smaller than that of the other sobemoviruses. The interactions of coat proteins in sobemovirus capsids involve calcium ions. Depletion of calcium ions results in particle swelling, which is considered a first step in disassembly. We could not identify any density for metal ions in the proximity of the conserved residues normally involved in calcium binding, but the RGMoV structure does not show any signs of swelling. A likely reason is the low pH (3.0) of the crystallization buffer in which the groups interacting with the calcium ions are not charged.

PubMed: 17881031
DOI: 10.1016/J.VIROL.2007.07.028

Experimental method

X-RAY DIFFRACTION (2.9 Å)