8PD0
cryo-EM structure of Doa10 in MSP1E3D1
Summary for 8PD0
| Entry DOI | 10.2210/pdb8pd0/pdb |
| EMDB information | 17597 |
| Descriptor | ERAD-associated E3 ubiquitin-protein ligase DOA10, 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE (3 entities in total) |
| Functional Keywords | erad, doa10, march6, teb4, retrotranslocation, ubiquitination, ubc6, sybody, sqle, squalenemonooxygenase, ligase |
| Biological source | Saccharomyces cerevisiae (baker's yeast) |
| Total number of polymer chains | 1 |
| Total formula weight | 154617.36 |
| Authors | |
| Primary citation | Botsch, J.J.,Junker, R.,Sorgenfrei, M.,Ogger, P.P.,Stier, L.,von Gronau, S.,Murray, P.J.,Seeger, M.A.,Schulman, B.A.,Brauning, B. Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE. Nat Commun, 15:410-410, 2024 Cited by PubMed Abstract: Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity. PubMed: 38195637DOI: 10.1038/s41467-023-44670-5 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (3.58 Å) |
Structure validation
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