Three-dimensional structure of satellite tobacco mosaic virus at 2.9 A resolution

The crystal structure of satellite tobacco mosaic virus (STMV) has been solved by a combination of multiple isomorphous replacement and molecular replacement methods and refined at 2.9 A resolution to a conventional R-factor of 0.215. STMV, a T = 1 icosahedral virus, is the smallest whose structure has been determined. The coat protein is an eight-stranded "Swiss roll" beta-barrel with an amino-terminal strand that extends away from the beta-barrel by more than 60 A. This strand is primarily responsible for quaternary interactions within the capsid. The most arresting feature of the virus structure is the intimate association of each capsid protein dimer with a Watson-Crick base-paired segment of RNA double helix on the interior of the virion. The icosahedral 2-fold axis of each dimer pair is coincident with that of the central base-pair of each helical RNA segment whose helical axis is along the edge of the icosahedron. The helical RNA segments are seven base-pairs in length with a stacked base at each 3' end so that a total of 16 nucleotides is clearly visible. The character of the RNA helix is somewhat different than any of the canonical forms. Assuming full occupancy, then approximately 45% of the total RNA genome is present in the electron density map. The close association of capsid with highly structured nucleic acid suggests that assembly of STMV is likely to be a highly co-operative process involving both protein and RNA. The nucleic acid is distributed within the virion with a high degree of order. The capsid protein is a true double helical RNA binding protein and a number of prominent interactions between protein and RNA can be clearly seen.