The estrogen receptor alpha (ER) is a member of a large nuclear hormone receptor family that regulates a network of genes to control cell homeostasis. Aberrant expression or point mutations of ER have been associated with several types of cancers, but a mechanistic understanding of ER function at the molecular level is still missing. Such knowledge will help to suggest novel therapeutic interventions. The ER mediates steroid control of transcription through the two domains: the DNA-binding domain (DBD) and the ligand-binding domain (LBD). The goal of our project is to eventually understand the allosteric cross-talk between these domains. Compelling evidence from several well-studied NRs indicates that interactions are formed between the two domains. However, it remains completely unknown how the two ER domains communicate with each other and identify protein regions that are involved in allosteric signaling. The ER is a homodimer with multiple domains, and structural flexibility, making it a challenging protein for high-resolution structural studies. To date, high-resolution structures of individual domains, but not of the ER complex containing both domains, have been determined. To understand how the DBD and the LBD interact with each other, we have been developing a multifaceted modeling method that combines information from small-angle X-ray scattering (SAXS) and synchrotron footprinting with the high-resolution structures of the individual domains. We have extensively tested and validated this methodology on a variety of systems with known protein complexes. We demonstrate that the combination of these complementary data yields derived complex structures that are close to the known crystal structures. Using these approaches, we have made significant progress in obtaining structural information for the estrogen receptor (ER) from experimental SAXS and footprinting measurements, and chemical cross-linking. These data will reveal information about the ER that has been unattainable through other methods and will identify interactions between the DBD and the LBD as well as previously uncharacterized DBD-LBD interfaces. We will also attempt to explain how several disease-associated ER mutations influence transcriptional potency of ER, and will provide a molecular characterization of the mutant ER complexes.