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The estrogen receptor-related receptorc (ERRc/ERR3/ NR3B3) is an orphan member of the nuclear receptor superfamily closely related to the estrogen receptors. To explore the DNA binding characteristics, the protein–DNA interaction was studied in electrophoretic mobility shift assays (EMSAs). In vitro translated ERRc binds as a homodimer to direct repeats (DR) without spacing of the nuclear receptor half-site 5¢-AGGTCA-3¢(DR-0), to exten-dedhalf-sites, and to the inverted estrogen response element | Eur. J. Biochem. 269 4086-4097 2002 FEBS 2002 doi 10.1046 j.1432-1033.2002.03102.x Domains of ERRc that mediate homodimerization and interaction with factors stimulating DNA binding Moritz Hentschke Ute Siisens and Uwe Borgmeyer Zentrum fur Molekulare Neurobiologie Hamburg ZMNH Universitat Hamburg Germany The estrogen receptor-related receptor y ERRy ERR3 NR3B3 is an orphan member of the nuclear receptor superfamily closely related to the estrogen receptors. To explore the DNA binding characteristics the protein-DNA interaction was studied in electrophoretic mobility shift assays EMSAs . In vitro translated ERRy binds as a homodimer to direct repeats DR without spacing of the nuclear receptor half-site 5 -AGGTCA-3 DR-0 to extended half-sites and to the inverted estrogen response element. Using ERRy deletion constructs binding was found to be dependent on the presence of sequences in the ligand binding domain LBD . A far-Western analysis revealed that ERRy forms dimers even in the absence of DNA. Two elements located in the hinge region and in the LBD respectively are necessary for DNA-independent dimerization. DNA binding of bacterial expressed ERRy requires additional factors present in the serum and in cellular extracts. Fusion proteins of the germ cell nuclear factor GCNF NR6A1 with ERRy showed that the characteristic feature to be stimulated by additional factors can be transferred to a heterologous protein. The stimulating activity was further characterized and its target sequence narrowed down to a small element in the hinge region. Keywords orphan nuclear receptor transcription factor estrogen receptor-related DNA binding dimerization. The nuclear receptors NR comprise a family of transcriptional regulators involved in a wide variety of biological processes such as embryonic development differentiation and homeostasis. This family includes ligand-dependent transcription factors for steroid hormones estrogens thyroid hormones retinoids vitamin D and other .