8C81 image
Deposition Date 2023-01-18
Release Date 2023-10-11
Last Version Date 2023-10-11
Entry Detail
PDB ID:
8C81
Keywords:
Title:
Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Protein ORM1
Gene (Uniprot):ORM1
Mutations:S51A, S52A, S53A
Chain IDs:A
Chain Length:222
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Serine palmitoyltransferase 1
Gene (Uniprot):LCB1
Chain IDs:B
Chain Length:580
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Serine palmitoyltransferase 2
Gene (Uniprot):LCB2
Chain IDs:C
Chain Length:561
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Serine palmitoyltransferase-regulating protein TSC3
Gene (Uniprot):TSC3
Chain IDs:D
Chain Length:80
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Molecule:Phosphatidylinositol-3-phosphatase SAC1
Gene (Uniprot):SAC1
Chain IDs:E
Chain Length:623
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
Structure of the ceramide-bound SPOTS complex.
Nat Commun 14 6196 6196 (2023)
PMID: 37794019 DOI: 10.1038/s41467-023-41747-z

Abstact

Sphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. Its activity is tightly regulated through multiple binding partners, including Tsc3, Orm proteins, ceramides, and the phosphatidylinositol-4-phosphate (PI4P) phosphatase Sac1. The structural organization and regulatory mechanisms of this complex are not yet understood. Here, we report the high-resolution cryo-EM structures of the yeast SPT in complex with Tsc3 and Orm1 (SPOT) as dimers and monomers and a monomeric complex further carrying Sac1 (SPOTS). In all complexes, the tight interaction of the downstream metabolite ceramide and Orm1 reveals the ceramide-dependent inhibition. Additionally, observation of ceramide and ergosterol binding suggests a co-regulation of sphingolipid biogenesis and sterol metabolism within the SPOTS complex.

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Primary Citation of related structures