The mechanism by which the naturally occurring ligand for a nuclear hormone receptor regulates transcription remains largely unknown. One approach combines the specificity of monoclonal antibodies, which recognize a three-dimensional epitope, with ligand binding. Using purified retinoic acid receptor gamma D and E domains, a panel of six unique monoclonal antibodies were isolated and characterized using solid-state receptor binding and retinoic acid receptor (RAR)-RXR heterodimer supershift formation. Three antibodies are specific for RARgamma (mAbI, mAbII, and mAbV) and four recognize a three-dimensional epitope (mAbI, mAbIV, mAbV, and mAbVI). Three antibodies (mAbIII, mAbV, and mAbVI) dissociate from the receptor in electrophoretic mobility shift assays upon the addition of retinoic acid. In particular, the binding characteristics of mAbIII, whose epitope was mapped to a region identified as an omega-loop (amino acids 207-222), suggest a model for ligand binding to the receptor. In this model, ligand binding causes a positioning of helix 12 into a favorable conformation for interaction with the transcriptional machinery. The Omega-loop then closes in order to stabilize this "active" position. The results reported here also suggest that a region of the hinge or D domain of the receptor (amino acids 156-188), an area that can play a role in protein-protein interactions, may also be important in ligand-induced functional changes.