Direct visualization of ERAD nanocompartments within the cell

ER-associated degradation (ERAD) is an evolutionarily-conserved quality control mechanism where misfolded proteins are removed from the endoplasmic reticulum (ER) and degraded by the ubiquitin-proteasome system. While many ERAD-mediating proteins have been identified, it is unknown how they are spatially organized within the cell. Using in situ cryo-electron tomography to image the native molecular landscape of Chlamydomonas, we discovered that ERAD proteins are concentrated within ~200 nm cytosolic foci that contact the ER membrane away from the ER-Golgi interface. These ribosome-excluding ERAD nanocompartments consist of a core of clustered proteasomes surrounded by Cdc48. Active proteasomes directly engage with the ER membrane, indicating an additional Cdc48-independent mechanism for extraction of misfolded proteins. Our study reveals that ERAD has precise cellular architecture, which likely enables efficient protein quality control.