Although structural studies on the ligand-binding domain (LBD) have established the general mode of nuclear receptor (NR)/coactivator interaction, determinants of binding specificity are only partially understood. The LBD of estrogen receptor-␣ (ER␣), for example, interacts only with a region of peroxisome proliferator-activated receptor coactivator (PGC)-1␣, which contains the canonical LXXLL motif (NR box2), whereas the LBD of estrogen-related receptor-␣ (ERR␣) also binds efficiently an untypical, LXXYL-containing region (NR box3) of PGC-1␣. Surprisingly, in a previous structural study, the ER␣ LBD has been observed to bind NR box3 of transcriptional intermediary factor (TIF)-2 untypically via LXXYL, whereas the ERR␣ LBD binds this region of TIF-2 only poorly. Here we present a new crystal structure of the ERR␣ LBD in complex with a PGC-1␣ box3 peptide. In this structure, residues N-terminal of the PGC-1␣ LXXYL motif formed contacts with helix 4, the loop connecting helices 8 and 9, and with the C terminus of the ERR␣ LBD. Interaction studies using wild-type and mutant PGC-1␣ and ERR␣ showed that these contacts are functionally relevant and are required for efficient ERR␣/PGC-1␣ interaction. Furthermore, a structure comparison between ERR␣ and ER␣ and mutation analyses provided evidence that the helix 8 -9 loop, which differs significantly in both nuclear receptors, is a major determinant of coactivator binding specificity. Finally, our results revealed that in ERR␣ the helix 8 -9 loop allosterically links the LBD homodimer interface with the coactivator cleft, thus providing a plausible explanation for distinct PGC-1␣ binding to ERR␣ monomers and homodimers.