It is known that estrogen receptors can function as nuclear receptors and transcription factors in the nucleus and as signaling molecules in the plasma membrane. In addition, the localization of the receptors in mitochondria suggests that they may play important roles in mitochondria. In order to identify novel proteins that are involved in ER␣-mediated actions of estrogens, we used a proteomic method that integrated affinity purification, two-dimensional gel electrophoresis, and mass spectrometry to isolate and identify cellular proteins that interact with ER␣. One of the proteins identified was trifunctional protein -subunit (HADHB), a mitochondrial protein that is required for -oxidation of fatty acids in mitochondria. We have verified the interaction between ER␣ and HADHB by coimmunoprecipitation and established that ER␣ directly binds to HADHB by performing an in vitro binding assay. In addition, we have shown that ER␣ colocalizes with HADHB in the mitochondria by confocal microscopy, and the two proteins interact with each other within mitochondria by performing coimmunoprecipitation using purified mitochondria as starting materials. We have demonstrated that the expression of ER␣ affects HADHB activity, and a combination of 17-estrodiol and tamoxifen affects the activity of HADHB prepared from human breast cancer cells that express ER␣ but not from the cells that are ER␣ deficient. Furthermore, we have demonstrated that 17-estrodiol plus tamoxifen affects the association of ER␣ with HADHB in human cell extract. Our results suggest that HADHB is a functional molecular target of ER␣ in the mitochondria, and the interaction may play an important role in the estrogen-mediated lipid metabolism in animals and humans. Molecular & Cellular Proteomics 11: 10.1074/mcp.M111.011056, 1-12, 2012.The biological activities of steroid hormone estrogens are mediated by two estrogen receptors (ERs), 1 ER␣ and ER, which are widely distributed in different tissues (1). Traditionally, ERs are considered nuclear receptors and classical transcription factors (2). Upon binding to estrogen, ERs undergo a conformational change, translocate to the nucleus, and regulate the expression of estrogen responsive genes through binding to estrogen response elements residing in those genes (3). Since its cloning in the 1980s (4), this classical mechanism has been studied extensively, and a large group of nuclear proteins called co-activators and co-repressors, which interact with ER␣, has been identified (5). Much less is known about the relatively newly cloned ER (6). Like the majority of other nuclear receptors, ER␣ and ER contain two activation domains, AF1 near the N terminus and AF2 in the ligand binding domain (7). The interactions between ER␣/ER and co-activators/co-repressors are normally mediated by the binding of the AF2 domain of ER␣/ER to one or more conserved pentapeptide LXXLL motifs (where X is any amino acid) in co-activators/co-repressors (5). In addition to the nucleus, ER␣ and ER are also found to be localized in...