125I-Apamin and photolabile derivatives of the toxin have been used to investigate the binding properties and subunit composition of small conductance Ca2+-activated potassium channels (SK(Ca) channels) expressed on plasma membranes from rat brain, rabbit liver, or rat pheochromocytoma (PC12) cells. On all preparations, 125I-apamin recognized single classes of acceptor binding sites with similar high affinity (Kd approximately 3-6 pM). Gallamine, however, was found to readily discriminate between 125I-apamin acceptors present in these preparations, showing a maximal approx nine-fold difference in affinity for acceptors expressed by rabbit liver or PC12 cells. Affinity-labeling patterns revealed the expression of different hetero-oligomeric combinations of high (86 or 59 kDa) and low (33 or 30 kDa) molecular mass 125I-apamin-binding polypeptides, consistent with pharmacological differences. Alternative expression of either 86- or 59-kDa polypeptides appeared to be the most important factor influencing gallamine's affinity for SK(Ca) channel subtypes. Both high- and low-molecular-mass polypeptides are integral membrane proteins, the latter being glycosylated in a tissue-specific manner.