Misfolded proteins in the endoplasmic reticulum (ER) are often degraded in the cytosol by a process called ER-associated protein degradation (ERAD). During ERAD in S. cerevisiae, the ATPase Cdc48p associates with Der1p, a putative component of a retro-translocation channel. Cdc48p also binds a homolog of Der1p, Dfm1p, that has no known function in ERAD. Here, we show that Der1p and Dfm1p are contained in distinct complexes. While the complexes share several ERAD components, only the Dfm1p complex contains the Cdc48p cofactors Ubx1p and Ubx7p, while the Der1p complex is enriched in Ufd1p. These data suggest distinct functions for the Der1p and Dfm1p complexes.
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