Tetrairidium, a four-atom cluster, is readily visible as a density label in three-dimensional cryo-EM maps of proteins at 10-25 angstrom resolution

Heavy metal clusters derivatized to bind to designated chemical groups on p roteins have great potential as density labels for cryo-electron microscopy . Smaller clusters offer higher resolution and penetrate more easily into s terically restricted sites, but are more difficult to detect. In this conte xt, we have explored the potential of tetrairidium (Ir-4) as a density labe l by attaching it via maleimide linkage to the C-terminus of the hepatitis B virus (HBV) capsid protein. Although the clusters are not visible in unpr ocessed cryo-electron micrographs, they are distinctly visible in three-dim ensional density maps calculated from them, even at only partial occupancy. The Ir-4 label was clearly visualized in our maps at 11-14 Angstrom resolu tion of both size variants of the HBV capsid, thus confirming our previous localization of this site with undecagold (Zlotnick, A., Cheng, N., Stahl, S. J., Conway, J. F., Steven, A. C.) and Wingfield, P. T, Proc. Natl. Acad. Sci. USA 94, 9556-9561, 1997). Ir-4 penetrated to the interior of intact c apsids to label this site on their inner surface, unlike undecagold for whi ch labelling was achieved only with dissociated dimers that were then reass embled into capsids. The Ir-4 cluster remained visible as the resolution of the maps was lowered progressively to similar to 25 Angstrom. (C) 1999 Aca demic Press.