8PD0 | pdb_00008pd0

cryo-EM structure of Doa10 in MSP1E3D1

• PDB DOI: https://doi.org/10.2210/pdb8PD0/pdb
• EM Map EMD-17597: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-06-11 Released: 2024-01-17 
• Deposition Author(s): Botsch, J.J., Braeuning, B., Schulman, B.A.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.58 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE.

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.

(2024) Nat Commun 15: 410-410

• PubMed: 38195637 
• DOI: https://doi.org/10.1038/s41467-023-44670-5
• Primary Citation Related Structures: 
  8PD0, 8PDA


• 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.

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Organizational Affiliation: 
• Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
Technical University of Munich, School of Natural Sciences, Munich, Germany.
Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland.
Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. [e-mail].
Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 154.62 kDa 
• Atom Count: 6,274 
• Modeled Residue Count: 880 
• Deposited Residue Count: 1,319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERAD-associated E3 ubiquitin-protein ligase DOA10	A	1,319	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SSM4, DOA10, YIL030C, YI3299.01C, YI9905.18C EC: 2.3.2.27
UniProt
Find proteins for P40318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40318  Go to UniProtKB:  P40318

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCW	B [auth A], C [auth A], D [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
PX6	E [auth A]	1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE C35 H68 O8 P PORPENFLTBBHSG-MGBGTMOVSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.58 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Botsch, J.J., Braeuning, B., Schulman, B.A.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release