8PDA image
Entry Detail
PDB ID:
8PDA
EMDB ID:
Keywords:
Title:
cryo-EM structure of Doa10 with RING domain in MSP1E3D1
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-06-12
Release Date:
2024-01-17
Method Details:
Experimental Method:
Resolution:
3.58 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:ERAD-associated E3 ubiquitin-protein ligase DOA10
Chain IDs:A
Chain Length:1319
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE.
Nat Commun 15 410 410 (2024)
PMID: 38195637 DOI: 10.1038/s41467-023-44670-5

Abstact

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.

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