Skip to main content

 8IAM | pdb_00008iam

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

Validation slider image for 8IAM

This is version 1.1 of the entry. See complete history. 

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 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.

Macromolecule Content 

  • Total Structure Weight: 315.99 kDa 
  • Atom Count: 20,192 
  • Modeled Residue Count: 2,536 
  • Deposited Residue Count: 2,782 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chimera of Long chain base biosynthesis protein 1 and Serine palmitoyltransferase 1
A, E
534Arabidopsis thaliana, Saccharomyces 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))
Explore P25045 
Go to UniProtKB:  P25045
Find proteins for Q94IB8 (Arabidopsis thaliana)
Explore Q94IB8 
Go to UniProtKB:  Q94IB8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ94IB8P25045
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore P40970 
Go to UniProtKB:  P40970
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40970
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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))
Explore Q06144 
Go to UniProtKB:  Q06144
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06144
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3E790
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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
  • Version 1.1: 2025-07-02
    Changes: Data collection, Structure summary