Vaccinia virus was treated in a controlled manner with various combinations of nonionic detergents, reducing agents, and proteolytic enzymes, and successive products of the reactions were visualized using atomic force microscopy (AFM). Following removal of the outer lipid/protein membrane, a layer 20 to 40 nm in thickness was encountered that was composed of fibrous elements which, under reducing conditions, rapidly decomposed into individual monomers on the substrate. Beneath this layer was the virus core and its prominent lateral bodies, which could be dissociated or degraded with proteases. The core, in addition to the lateral bodies, was composed of a thick, multilayered shell of proteins of diverse sizes and shapes. The shell, which was readily etched with proteases, was thoroughly permeated with pores, or channels. Prolonged exposure to proteases and reductants produced disgorgement of the viral DNA from the remainders of the cores and also left residual, flattened, protease-resistant sacs on the imaging substrate. The DNA was readily visualized by AFM, which revealed some regions to be "soldered" by proteins, others to be heavily complexed with protein, and yet other parts to apparently exist as bundled, naked DNA. Prolonged exposure to proteases deproteinized the DNA, leaving masses of extended, free DNA. Estimates of the interior core volume suggest moderate but not extreme compaction of the genome.Vaccinia virus, the best-characterized member of the Poxviridae family, is unusual among most double-stranded DNA viruses in that both transcription and replication occur in the cytoplasm of the host cell (5,8,24). The 191-kbp genome of the Copenhagen strain contains up to 266 open reading frames encoding proteins Ͼ65 amino acids in length (9, 15), with 63 to 80 vaccinia virus gene products being packaged in the virion (4,53,57,60). Replication takes place within discrete cytoplasmic viral factories that are thought to be devoid of cellular organelles (3) but which contain ribosomes (16). Infectious virions can be isolated in several forms, depending on their degree of maturation, including mature virus (MV), wrapped virus, and enveloped virus (25).Many general features of vaccinia virion architecture are readily apparent from a variety of studies (3), notably a genome/enzyme-containing proteinaceous core, proteinaceous lateral bodies (LBs), and surrounding surface tubular elements and lipid membrane. Nonetheless, despite ϳ60 years of study by conventional electron microscopy (EM) (11,14,15,45,48,54,58), cryoelectron microscopy (1, 9, 54), and more recently cryoelectron tomography (4) freeze etch (31), deep etch (11), and atomic force (22) microscopies, specific controversies remain in issues such as the intrinsic rigidity of the core, the degree of order in genome packaging, the degree and affinity of the association of the genome with protein in the packaged state, the presence/absence of an "inner membrane" or "palisade" enwrapping the core, and the number of lipid bilayers that enwrap the intact virion. S...