Acetylation is correlated with chromatin decondensation and transcriptional activation, but its regulation by histone deacetylase (HDAC)-bearing corepressor complexes is poorly understood. Here, we describe the mechanism of assembly of the mammalian Sin3L/Rpd3L complex facilitated by Sds3, a conserved subunit deemed critical for proper assembly. Sds3 engages a globular, helical region of the HDAC interaction domain (HID) of the scaffolding protein Sin3A through a bipartite motif comprising a helix and an adjacent extended segment. Sds3 dimerizes through not only one of the predicted coiled-coil motifs but also, the segment preceding it, forming an ∼150-Å-long antiparallel dimer. Contrary to previous findings in yeast, Sin3A rather than Sds3 functions in recruiting HDAC1 into the complex by engaging the latter through a highly conserved segment adjacent to the helical HID subdomain. In the resulting model for the ternary complex, the two copies of the HDACs are situated distally and dynamically because of a natively unstructured linker connecting the dimerization domain and the Sin3A interaction domain of Sds3; these features contrast with the static organization described previously for the NuRD (nucleosome remodeling and deacetylase) complex. The Sds3 linker features several conserved basic residues that could potentially maintain the complex on chromatin by nonspecific interactions with DNA after initial recruitment by sequence-specific DNA-binding repressors.transcription repression | histone deacetylase | corepressor complex | protein-protein interaction | structural biology H istone deacetylation constitutes the primary mechanism of erasing acetylation marks on histones, leading to a chromatin environment that is repressive to gene transcription. Histone deacetylases (HDACs) exhibit limited substrate specificity and rely on transcription factors with sequence-specific DNAbinding and/or chromatin-binding activities for their targeting specificity. Among 11 known Zn 2+ -dependent HDACs in mammals, only HDAC1, HDAC2, and HDAC3 are constitutively nuclear, regulating the transcription of a broad array of genes that impact fundamentally on cellular physiology and organism development (1-3). These HDACs are commonly found in multiprotein corepressor complexes, with the closely related HDAC1 and HDAC2 partitioning broadly into the Sin3L/Rpd3L, Sin3S/ Rpd3S, NuRD (nucleosome remodeling and deacetylase), and CoREST (corepressor of REST transcription factor) complexes, whereas HDAC3 is found exclusively in SMRT/NCoR (silencing mediator of retinoid and thyroid hormone receptor/nuclear receptor corepressor) complexes. Little is known regarding the structure and organization of these complexes, although molecular insights into HDAC recruitment into these complexes are beginning to emerge.High-resolution structures of HDAC1 and HDAC3 in complex with the MTA1 (metastatic tumor antigen 1) and SMRT subunits in the NuRD and SMRT/NCoR complexes, respectively (4, 5), revealed a shared structural theme involving the catalytic do...