Subunit interactions in southern bean mosaic virus

Abstract

The structures of the three quasi-equivalent subunits A, B and C of southern bean mosaic virus have been carefully built in accordance with an electron density map that had been refined with three cycles of molecular replacement averaging. The map was interpreted with the aid of the amino acid sequence and a computer graphics system. The three quasi-equivalent subunits were compared in pairs and found to have almost the same conformation except for five residues in the carboxy-terminal vestigial “hinge”. Contacts between subunits in the capsid were tabulated and analyzed. The largest number of interactions was between the 5-fold-related subunits. although the quasi-3-fold or quasi-6-fold-related subunits had nearly the same number of contacts. The interactions across the 2-fold axes were far fewer. A number of charge interactions and numerous hydrogen-bonding possibilities exist in the subunit interactions. The icosahedral 5-fold interactions between A subunits (AA 5 ) and the quasi-6-fold interactions between C and B subunits without the interposed βA arm (CB 5 ) are essentially identical. The quasi-6-fold interactions containing the interposed ordered βA arm of the C subunit (B 2 C) are quite different. There is a “vector of rotation” or line of contact about which the C and B subunits rotate to form either CB 5 or B 2 C interactions. A similar situation pertains to the relationship between the quasi-2-fold contacts AB 5 and the icosahedral 2-fold contacts CC 2 . The amount of rotation about the hinge is 36° to 39° in both cases. The quasi-3-fold contacts BA and AC are essentially identical but differ slightly but significantly from the BC contacts. The latter have an additional 5° rotation between subunits. It is proposed that the “relaxed” AB 5 conformation of subunit dimers might self-assemble into 10mer caps composed of five dimers about a 5-fold axis with RNA binding to the basic random domain and the basic interior surface of the shell domain. This 10mer might nucleate the assembly of a T =1 or T =3 capsid, depending on the charge state of carboxyl group clusters in the subunit contact region. In the low charge state, T =1 capsids are formed. Alternatively, in the high charge state, dimers must be “tensed”, as in the CC 2 contacts of the native virus, for binding to the 10mer cap, creating a hydrophobic channel to induce the ordering of the βA arm and formation of the β-annulus. The two-state condition of dimers in a viral coat protein extends the range of structures originally envisaged by Caspar & Klug (1962) . Appendix I considers a possible manner in which viral RNA might interact with the coat protein. A pattern of basic residues on the southern bean mosaic virus coat protein surface facing the RNA is able to dock a nine base-pair double-helical A -RNA structure with surprising accuracy. The basic residues are each associated with a different phosphate and the protein can make interactions with five bases in the minor groove. It is proposed that this is one of a small number of ways in which the RNA interacts with southern bean mosaic virus coat protein.