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- PDB-8qtr: Cryo-EM structure of the FB-bound yeast Ceramide Synthase -

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Entry
Database: PDB / ID: 8qtr
TitleCryo-EM structure of the FB-bound yeast Ceramide Synthase
Components(Ceramide synthase ...) x 3
KeywordsMEMBRANE PROTEIN / Ceramide Synthase
Function / homology
Function and homology information


very-long-chain ceramide synthase / acyl-CoA ceramide synthase complex / Sphingolipid de novo biosynthesis / sphingosine N-acyltransferase activity / ceramide biosynthetic process / nuclear periphery / nuclear envelope / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
TRAM/LAG1/CLN8 homology domain / Sphingosine N-acyltransferase Lag1/Lac1-like / TLC domain / TLC domain profile. / TRAM, LAG1 and CLN8 homology domains.
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / hexacosanoic acid / AMMONIUM ION / : / : / Ceramide synthase LAC1 / Ceramide synthase LAG1 / Ceramide synthase subunit LIP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSchaefer, J. / Clausmeyer, L. / Koerner, C. / Moeller, A. / Froehlich, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure of the yeast ceramide synthase.
Authors: Jan-Hannes Schäfer / Lena Clausmeyer / Carolin Körner / Bianca M Esch / Verena N Wolf / Jennifer Sapia / Yara Ahmed / Stefan Walter / Stefano Vanni / Dovile Januliene / Arne Moeller / Florian Fröhlich /
Abstract: Ceramides are essential lipids involved in forming complex sphingolipids and acting as signaling molecules. They result from the N-acylation of a sphingoid base and a CoA-activated fatty acid, a ...Ceramides are essential lipids involved in forming complex sphingolipids and acting as signaling molecules. They result from the N-acylation of a sphingoid base and a CoA-activated fatty acid, a reaction catalyzed by the ceramide synthase (CerS) family of enzymes. Yet, the precise structural details and catalytic mechanisms of CerSs have remained elusive. Here we used cryo-electron microscopy single-particle analysis to unravel the structure of the yeast CerS complex in both an active and a fumonisin B1-inhibited state. Our results reveal the complex's architecture as a dimer of Lip1 subunits bound to the catalytic subunits Lag1 and Lac1. Each catalytic subunit forms a hydrophobic crevice connecting the cytosolic site with the intermembrane space. The active site, located centrally in the tunnel, was resolved in a substrate preloaded state, representing one intermediate in ceramide synthesis. Our data provide evidence for competitive binding of fumonisin B1 to the acyl-CoA-binding tunnel.
History
DepositionOct 13, 2023Deposition site: PDBE / Processing site: PDBE
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ceramide synthase LAG1
B: Ceramide synthase LAC1
C: Ceramide synthase subunit LIP1
D: Ceramide synthase subunit LIP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,56316
Polymers103,6484
Non-polymers6,91512
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Ceramide synthase ... , 3 types, 4 molecules ABCD

#1: Protein Ceramide synthase LAG1


Mass: 37150.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LAG1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38703
#2: Protein Ceramide synthase LAC1


Mass: 35802.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LAC1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P28496
#3: Protein Ceramide synthase subunit LIP1


Mass: 15347.415 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LIP1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03579

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Non-polymers , 5 types, 12 molecules

#4: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-WXE / Macrofusine / (2R)-2-[2-[(5S,6S,7R,9S,11S,16S,18R,19S)-19-azanyl-6-[(3S)-3-carboxy-5-oxidanyl-5-oxidanylidene-pentanoyl]oxy-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid / Fumonisin b1


Mass: 721.830 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H59NO15 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-7PO / hexacosanoic acid


Mass: 396.690 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H52O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PIJ / [(2S)-1-hexadecanoyloxy-3-[hydroxy-[(2S,3R,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] heptadecanoate


Mass: 825.059 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81O13P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Heterotetrameric complex of yeast ceramide synthase with Lag1, Lac1 and Lip1
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 259645 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028034
ELECTRON MICROSCOPYf_angle_d0.51310833
ELECTRON MICROSCOPYf_dihedral_angle_d15.3441310
ELECTRON MICROSCOPYf_chiral_restr0.0411153
ELECTRON MICROSCOPYf_plane_restr0.0041287

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