Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex

• Published in: Science (American Association for the Advancement of Science) Vol. 368; no. 6489
• Main Authors: Wu, Xudong, Siggel, Marc, Ovchinnikov, Sergey, Mi, Wei, Svetlov, Vladimir, Nudler, Evgeny, Liao, Maofu, Hummer, Gerhard, Rapoport, Tom A.
• Format: Journal Article
• Language: English
• Published: United States The American Association for the Advancement of Science 24.04.2020
• Subjects: Adenosine; Adenosine triphosphatase; Binding sites; Biodegradation; Carrier Proteins - chemistry; Carrier Proteins - metabolism; Channels; Computer simulation; Control systems; Crosslinking; Cryoelectron Microscopy; Cytosol; Cytotoxicity; Degradation; Domains; Electron microscopy; Endoplasmic reticulum; Endoplasmic Reticulum - metabolism; Endoplasmic Reticulum-Associated Degradation; Gates; Glycan; Glycoproteins; Glycosidases; Grooves; Homeostasis; Homology; Hydrophobicity; Inserts; Intermediates; Lipids; Macromolecules; Mannose; Membrane Glycoproteins - chemistry; Membrane Glycoproteins - metabolism; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Membranes; Microscopy; Molecular dynamics; Molecular Dynamics Simulation; Multiprotein Complexes - chemistry; Multiprotein Complexes - metabolism; Phospholipids; Polypeptides; Proteasomes; Protein Domains; Protein Folding; Protein transport; Proteins; Proteolysis; Quality control; Residues; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; Substrates; Translocation; Triphosphatase; Ubiquitin; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - chemistry; Yeast
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.aaz2449

Misfolded endoplasmic reticulum (ER) proteins are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome in a process known as ER-associated protein degradation (ERAD). ERAD of misfolded luminal ER proteins (ERAD-L) is mediated by the Hrd1 complex, composed of the ubiquitin ligase Hrd1 and four additional proteins (Hrd3, Der1, Usa1, and Yos9). Wu et al. report a cryo–electron microscopy structure of the active Hrd1 complex from yeast and, based on this structure, developed a model for how substrates are recognized and retrotranslocated. They propose that Hrd3 and Yos9 jointly create a luminal binding site for misfolded glycoproteins. Hrd1 and Der1 form “half-channels” juxtaposed in a thinned section of the ER membrane, which allows a polypeptide loop of an ERAD-L substrate to move through it. Science , this issue p. eaaz2449 The Hrd1 complex retrotranslocates misfolded luminal endoplasmic reticulum proteins through “half-channels” juxtaposed in a thinned membrane. Misfolded luminal endoplasmic reticulum (ER) proteins undergo ER-associated degradation (ERAD-L): They are retrotranslocated into the cytosol, polyubiquitinated, and degraded by the proteasome. ERAD-L is mediated by the Hrd1 complex (composed of Hrd1, Hrd3, Der1, Usa1, and Yos9), but the mechanism of retrotranslocation remains mysterious. Here, we report a structure of the active Hrd1 complex, as determined by cryo–electron microscopy analysis of two subcomplexes. Hrd3 and Yos9 jointly create a luminal binding site that recognizes glycosylated substrates. Hrd1 and the rhomboid-like Der1 protein form two “half-channels” with cytosolic and luminal cavities, respectively, and lateral gates facing one another in a thinned membrane region. These structures, along with crosslinking and molecular dynamics simulation results, suggest how a polypeptide loop of an ERAD-L substrate moves through the ER membrane.