THE STRUCTURE OF SIMIAN-VIRUS-40 REFINED AT 3.1 ANGSTROM RESOLUTION

Background: The structure of simian virus 40 (SV40), previously determ ined at 3.8 Angstrom resolution, shows how its pentameric VP1 assembly units are tied together by extended C-terminal arms. In order to defi ne more precisely the possible assembly mechanisms, we have refined th e structure at 3.1 Angstrom resolution. Results: New data from a high- intensity synchrotron source have been used for phase extension by ele ctron-density averaging and refinement, exploiting only the strict 5-f old non-crystallographic symmetry for the real-space averaging steps. The accurate model enables us to study important structural features o f the virus particle in detail. The remarkably invariant core of the V P1 pentamer bears the docking sites for the C-terminal arms from other pentamers. These contacts are the principal way in which pentameric a ssembly units are linked together in the capsid. Only at the interface between five-coordinated and six-coordinated pentamers do the pentame r cores appear to interact strongly. There are two cation-binding site s per VP1 monomer, seen in a soaking experiment with gadolinium nitrat e. These sites are quite close to each other at the interfaces between pentamers. Conclusions: We propose that the contact between five-coor dinated and six-coordinated pentamers may help to generate a six-penta mer nucleus, with which further pentamers can assemble to generate the complete particle. Calcium ions probably stabilize the structure of t he assembled particle, rather than direct its assembly.