The binding of [H-3](R)alpha-methylhistamine, a potent and specific agonist at histamine H-3 receptors, was investigated with membranes of rat cerebral cortex. In phosphate buffer the specific binding defined with thioperamide, an H-3 receptor antagonist, displayed characters of reversibility and saturability with a B(max) of approximately 30 fmol/mg protein. The K(D), derived from either dissociation/association rates or saturation kinetics at equilibrium, was approximately 0.5 nM at 25-degrees-C. Competition studies indicated that the binding occurred with a stereoselectivity and pharmacological specificity similar to that of functional H-3 autoreceptors regulating histamine release in brain slices. However, whereas the potency of antagonists was closely similar in the two assay systems, that of agonists was approximately 10-fold higher in the binding assay. Among antagonists burimamide was the only one to compete with a pseudo-Hill coefficient significantly different from unity (n(H) = 0.48 +/- 0.03), indicating a possible heterogeneity among binding sites. The presence of 2.6 mM Ca2+, in a modified Krebs-Ringer medium, promoted the conversion of a large fraction of sites into a low-affinity component with a K(D) of 16 nM. The presence of guanylnucleotides in the Krebs-Ringer medium with Ca2+ abolished the binding to this low-affinity component whereas in a phosphate buffer only the K(D) was slightly increased. It is concluded that the H-3 receptor, like many other amine receptors, is coupled to its still unidentified effector system via a G-protein and regulated by Ca2+. However, unlike the latter, the H-3 receptor is down-regulated by the divalent cation.