8C81

Cryo-EM structure of the yeast SPT-Orm1-Sac1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of the ceramide-bound SPOTS complex.

Schafer, J.H.Korner, C.Esch, B.M.Limar, S.Parey, K.Walter, S.Januliene, D.Moeller, A.Frohlich, F.

(2023) Nat Commun 14: 6196-6196

  • DOI: https://doi.org/10.1038/s41467-023-41747-z
  • Primary Citation of Related Structures:  
    8C80, 8C81, 8C82

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Osnabrück University Department of Biology/Chemistry Structural Biology section, 49076, Osnabrück, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ORM1222Saccharomyces cerevisiaeMutation(s): 3 
Gene Names: ORM1YGR038W
Membrane Entity: Yes 
UniProt
Find proteins for P53224 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP53224
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase 1580Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LCB1END8TSC2YMR296C
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt
Find proteins for P25045 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP25045
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase 2561Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LCB2SCS1TSC1YDR062WD4246YD9609.16
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt
Find proteins for P40970 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40970
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase-regulating protein TSC380Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TSC3YBR058C-A
Membrane Entity: Yes 
UniProt
Find proteins for Q3E790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ3E790
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol-3-phosphatase SAC1623Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SAC1RSD1YKL212W
EC: 3.1.3.64
Membrane Entity: Yes 
UniProt
Find proteins for P32368 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP32368
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q7G
Query on Q7G

Download Ideal Coordinates CCD File 
H [auth A]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
C56 H92 O25
LKBFXDNKNZXHHW-NXLTVWPKSA-N
Z8A (Subject of Investigation/LOI)
Query on Z8A

Download Ideal Coordinates CCD File 
G [auth A]N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide
C44 H89 N O4
GKRXVCWVXYHWOD-KZRDWULCSA-N
ERG
Query on ERG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
J [auth B]
ERGOSTEROL
C28 H44 O
DNVPQKQSNYMLRS-APGDWVJJSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
K [auth C]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB944
German Research Foundation (DFG)GermanySFB15

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release