Electron dense material is present on both the presynaptic side and the postsynaptic side of many synapses when viewed in the electron microscope. Interestingly, both the presynaptic density associated with the active zone and the postsynaptic density vary in morphology at different types of synapses. Zhai and Bellen have a very nice review on the subject.
Figure 1. Variety in morphology of presynaptic densities Left: cortical synapses with robust postsynaptic densities and minor presynaptic densities (J. Spacek, Atlas of Ultrastructural Neurocytology). Middle left: a ribbon synapse from a cone cell (U. Matthews). Middle right: a Drosophila NMJ with two T-bar presynaptic specializations (courtesy of A. DiAntonio), and Right: a C. elegans NMJ with a large presynaptic density (S. Koushika).
At the molecular level, numerous components have been identified that localize to, or in the local environs of, the active zone. In vertebrates, these include Rim, Bassoon, Piccolo, ELKS/CAST, mUNC-13 and calcium channels. Most of these proteins are also found in C. elegans. Specifically, Rim, ELKS, and UNC-13 have all been defined as active zone proteins in C. elegans. The role of some of these proteins, like UNC-13, is at least roughly defined. Evidence from both C. elegans and vertebrates indicates that this protein is required for the priming step of the synaptic vesicle cycle. Rim appears to regulate priming of vesicles, but is not essential for that step. Bassoon partially disrupts synaptic transmission, but the specific role it plays is less clear. And of course, calcium channels provide a critical source of calcium at release sites, though perhaps not the only source for calcium. The roles of other proteins is less well defined.
Though some proteins localized at active zones have been identified, many others are likely undefined. For example, no mutant disrupting an active zone protein actually alters the physical structure of the zone to any significant degree. Furthermore, we have little idea how these proteins actually are trafficked to the synapse or tethered to the site. Though the functional roles of these proteins are beginning to be elucidated, the mechanism by which these proteins are maintained and restricted to the active zone are not known. My lab is addressing these issues in the worm using molecular genetics.