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Structure paper

TitleStructure of the ceramide-bound SPOTS complex.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 6196, Year 2023
Publish dateOct 4, 2023
AuthorsJan-Hannes Schäfer / Carolin Körner / Bianca M Esch / Sergej Limar / Kristian Parey / Stefan Walter / Dovile Januliene / Arne Moeller / Florian Fröhlich /
PubMed AbstractSphingolipids are structural membrane components that also function in cellular stress responses. The serine palmitoyltransferase (SPT) catalyzes the rate-limiting step in sphingolipid biogenesis. ...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.
External linksNat Commun / PubMed:37794019 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 3.4 Å
Structure data

16467

8c80

EMDB-16467, PDB-8c80:
Cryo-EM structure of the yeast SPT-Orm1-Monomer complex
Method: EM (single particle) / Resolution: 3.4 Å

16468

8c81

EMDB-16468, PDB-8c81:
Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex
Method: EM (single particle) / Resolution: 3.3 Å

16469

8c82

EMDB-16469, PDB-8c82:
Cryo-EM structure of the yeast SPT-Orm1-Dimer complex
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-16485: Cryo-EM structure of the yeast SPT-Orm1-Dimer complex, local refinement of a monomer
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-ERG:
ERGOSTEROL

ChemComp-Z8A:
N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

ChemComp-Q7G:
2-{[(4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsTRANSFERASE / Serine-Palmitoyl-Transferase / SPT / Orm-Protein

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