8IAM

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3D) complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Collaborative regulation of yeast SPT-Orm2 complex by phosphorylation and ceramide.

Xie, T.Dong, F.Han, G.Wu, X.Liu, P.Zhang, Z.Zhong, J.Niranjanakumari, S.Gable, K.Gupta, S.D.Liu, W.Harrison, P.J.Campopiano, D.J.Dunn, T.M.Gong, X.

(2024) Cell Rep 43: 113717-113717

  • DOI: https://doi.org/10.1016/j.celrep.2024.113717
  • Primary Citation of Related Structures:  
    8IAJ, 8IAK, 8IAM

  • PubMed Abstract: 

    The homeostatic regulation of serine palmitoyltransferase (SPT) activity in yeast involves N-terminal phosphorylation of Orm proteins, while higher eukaryotes lack these phosphorylation sites. Although recent studies have indicated a conserved ceramide-mediated feedback inhibition of the SPT-ORM/ORMDL complex in higher eukaryotes, its conservation and relationship with phosphorylation regulation in yeast remain unclear. Here, we determine the structure of the yeast SPT-Orm2 complex in a dephosphomimetic state and identify an evolutionarily conserved ceramide-sensing site. Ceramide stabilizes the dephosphomimetic Orm2 in an inhibitory conformation, facilitated by an intramolecular β-sheet between the N- and C-terminal segments of Orm2. Moreover, we find that a phosphomimetic mutant of Orm2, positioned adjacent to its intramolecular β-sheet, destabilizes the inhibitory conformation of Orm2. Taken together, our findings suggest that both Orm dephosphorylation and ceramide binding are crucial for suppressing SPT activity in yeast. This highlights a distinctive regulatory mechanism in yeast involving the collaborative actions of phosphorylation and ceramide.


  • Organizational Affiliation

    Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1
A, E
534Arabidopsis thalianaSaccharomyces cerevisiae S288C
This entity is chimeric
Mutation(s): 0 
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt
Find proteins for P25045 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P25045
Find proteins for Q94IB8 (Arabidopsis thaliana)
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Go to UniProtKB:  Q94IB8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ94IB8P25045
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase 2
B, F
561Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LCB2
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt
Find proteins for P40970 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P40970
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UniProt GroupP40970
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ORM2C [auth D],
G [auth H]
216Saccharomyces cerevisiae S288CMutation(s): 3 
Gene Names: ORM2
Membrane Entity: Yes 
UniProt
Find proteins for Q06144 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q06144
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UniProt GroupQ06144
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase-regulating protein TSC3D [auth C],
H [auth G]
80Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TSC3
Membrane Entity: Yes 
UniProt
Find proteins for Q3E790 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E790 
Go to UniProtKB:  Q3E790
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UniProt GroupQ3E790
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release