title: Refined structure of southern bean mosaic virus at 2.9 A resolution.
abstract: The T = 3 capsid of southern bean mosaic virus is analyzed in detail. The beta-sheets of the beta-barrel folding motif that form the subunits show a high degree of twist, generated by several beta-bulges. Only 34 water molecules were identified in association with the three quasi-equivalent subunits, most of them on the external viral surface. Subunit contacts related by quasi-3-fold axes are similar, are dominated by polar interactions and have almost identical calcium binding sites. There is no metal ion on the quasi-3-fold axis, as previously reported. Subunits related by quasi-2-fold and icosahedral 2-fold axes have different contacts but nevertheless display almost identical interactions between the antiparallel helices alpha A. A dipole-dipole type interaction between these helices may produce an energetically stable hinge that allows two types of dimers in a T = 3 assembly. The temperature factor distribution, the hydrogen-bonding pattern, and the contacts across the icosahedral 2-fold axes suggest that one of the dimer types is present in the intact virion and probably also in solution; the other is produced only during capsid assembly. Interactions along the 5-fold axes are mainly polar and possibly form an ion channel. The beta-sheet structures of the three subunits can be superimposed with considerable precision. Significant relative distortions between quasi-equivalent subunits occur mainly in helices and loops. The two dimeric forms and the subunit distortions are the consequence of the non-equivalent subunit environments in the capsid.
authors: Departamento de Fisica, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Argentina.
authors: A M
authors: AM
authors: Silva
authors: M G
authors: MG
authors: Rossmann
mesh_terms: D000595:Amino Acid Sequence; D002213:Capsid / Q000648:ultrastructure*; D006860:Hydrogen Bonding; D046911:Macromolecular Substances; D008958:Models, Molecular; D009029:Mosaic Viruses / Q000648:ultrastructure*; D011487:Protein Conformation
chemical_list: D046911:Macromolecular Substances