8QOF

Cryo-EM structure of the yeast SPT-Orm2-Dimer 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

The structure of the Orm2-containing serine palmitoyltransferase complex reveals distinct inhibitory potentials of yeast Orm proteins.

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

(2024) Cell Rep 43: 114627-114627

  • DOI: https://doi.org/10.1016/j.celrep.2024.114627
  • Primary Citation of Related Structures:  
    8QOF, 8QOG

  • PubMed Abstract: 

    Sphingolipid levels are crucial determinants of neurodegenerative disorders and therefore require tight regulation. The Orm protein family and ceramides inhibit the rate-limiting step of sphingolipid biosynthesis-the condensation of L-serine and palmitoyl-coenzyme A (CoA). The yeast isoforms Orm1 and Orm2 form a complex with the serine palmitoyltransferase (SPT). While Orm1 and Orm2 have highly similar sequences, they are differentially regulated, though the mechanistic details remain elusive. Here, we determine the cryoelectron microscopy structure of the SPT complex containing Orm2. Complementary in vitro activity assays and genetic experiments with targeted lipidomics demonstrate a lower activity of the SPT-Orm2 complex than the SPT-Orm1 complex. Our results suggest a higher inhibitory potential of Orm2, despite the similar structures of the Orm1- and Orm2-containing complexes. The high conservation of SPT from yeast to man implies different regulatory capacities for the three human ORMDL isoforms, which might be key for understanding their role in sphingolipid-mediated neurodegenerative disorders.


  • Organizational Affiliation

    Bioanalytical Chemistry Section, Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase 1A [auth B],
B [auth F]
580Saccharomyces 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))
Explore P25045 
Go to UniProtKB:  P25045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25045
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase-regulating protein TSC3C [auth D],
D [auth H]
80Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TSC3YBR058C-A
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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ORM2 isoform 1E [auth A],
F [auth E]
216Saccharomyces cerevisiaeMutation(s): 3 
Gene Names: ORM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Serine palmitoyltransferase 2G,
H [auth C]
561Saccharomyces 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))
Explore P40970 
Go to UniProtKB:  P40970
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40970
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q7G (Subject of Investigation/LOI)
Query on Q7G

Download Ideal Coordinates CCD File 
L [auth G],
N [auth C]
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
WAR (Subject of Investigation/LOI)
Query on WAR

Download Ideal Coordinates CCD File 
I [auth A],
J [auth E]
~{N}-[(2~{S},3~{S},4~{R})-1,3,4-tris(oxidanyl)octadecan-2-yl]heptacosanamide
C45 H91 N O4
GQBDWMHDFCUVJD-LKFPOFNCSA-N
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
K [auth G],
M [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

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB1557

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-04
    Type: Initial release