7YJN

Cryo-EM structure of the monomeric atSPT-ORM1 (ORM1-N17A) complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of sphingolipid homeostasis revealed by structural analysis of Arabidopsis SPT-ORM1 complex.

Liu, P.Xie, T.Wu, X.Han, G.Gupta, S.D.Zhang, Z.Yue, J.Dong, F.Gable, K.Niranjanakumari, S.Li, W.Wang, L.Liu, W.Yao, R.Cahoon, E.B.Dunn, T.M.Gong, X.

(2023) Sci Adv 9: eadg0728-eadg0728

  • DOI: https://doi.org/10.1126/sciadv.adg0728
  • Primary Citation of Related Structures:  
    7YJK, 7YJM, 7YJN, 7YJO

  • PubMed Abstract: 

    The serine palmitoyltransferase (SPT) complex catalyzes the first and rate-limiting step in sphingolipid biosynthesis in all eukaryotes. ORM/ORMDL proteins are negative regulators of SPT that respond to cellular sphingolipid levels. However, the molecular basis underlying ORM/ORMDL-dependent homeostatic regulation of SPT is not well understood. We determined the cryo-electron microscopy structure of Arabidopsis SPT-ORM1 complex, composed of LCB1, LCB2a, SPTssa, and ORM1, in an inhibited state. A ceramide molecule is sandwiched between ORM1 and LCB2a in the cytosolic membrane leaflet. Ceramide binding is critical for the ORM1-dependent SPT repression, and dihydroceramides and phytoceramides differentially affect this repression. A hybrid β sheet, formed by the amino termini of ORM1 and LCB2a and induced by ceramide binding, stabilizes the amino terminus of ORM1 in an inhibitory conformation. Our findings provide mechanistic insights into sphingolipid homeostatic regulation via the binding of ceramide to the SPT-ORM/ORMDL complex that may have implications for plant-specific processes such as the hypersensitive response for microbial pathogen resistance.


  • Organizational Affiliation

    Department of Chemical Biology, Department of 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
Long chain base biosynthesis protein 1420Arabidopsis thalianaMutation(s): 0 
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt
Find proteins for Q94IB8 (Arabidopsis thaliana)
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Go to UniProtKB:  Q94IB8
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UniProt GroupQ94IB8
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Long chain base biosynthesis protein 2a489Arabidopsis thalianaMutation(s): 0 
Gene Names: LCB2aLCB2
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt
Find proteins for Q9LSZ9 (Arabidopsis thaliana)
Explore Q9LSZ9 
Go to UniProtKB:  Q9LSZ9
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UniProt GroupQ9LSZ9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ORMDL family proteinC [auth D]157Arabidopsis thalianaMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for Q9C5I0 (Arabidopsis thaliana)
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Go to UniProtKB:  Q9C5I0
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UniProt GroupQ9C5I0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Long chain base biosynthesis protein 1D [auth E]62Arabidopsis thalianaMutation(s): 0 
Gene Names: LCB1EMB2779FBR11At4g36480AP22C7A10.880
EC: 2.3.1.50
Membrane Entity: Yes 
UniProt
Find proteins for Q94IB8 (Arabidopsis thaliana)
Explore Q94IB8 
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UniProt GroupQ94IB8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein, putative (DUF3317)E [auth C]77Arabidopsis thalianaMutation(s): 0 
Gene Names: At1g06515
Membrane Entity: Yes 
UniProt
Find proteins for A8MSB8 (Arabidopsis thaliana)
Explore A8MSB8 
Go to UniProtKB:  A8MSB8
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UniProt GroupA8MSB8
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-04-19
    Changes: Database references
  • Version 1.3: 2024-03-20
    Changes: Data collection, Source and taxonomy