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- PDB-9xd0: Structure of a membrane-bound inositol phosphorylceramide synthas... -

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Basic information

Entry
Database: PDB / ID: 9xd0
TitleStructure of a membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
Components
  • Aureobasidin-A
  • Inositol phosphorylceramide synthase catalytic subunit AUR1
  • Inositol phosphorylceramide synthase regulatory subunit KEI1
KeywordsTRANSFERASE / membrane protein / inositol phosphorylceramide synthase / LIPID BINDING PROTEIN
Function / homology
Function and homology information


inositol phosphorylceramide synthase / mannosyl diphosphorylinositol ceramide metabolic process / inositol phosphoceramide synthase activity / inositol phosphoceramide synthase complex / inositol phosphoceramide synthase regulator activity / inositol phosphoceramide metabolic process / sphingolipid biosynthetic process / Golgi cisterna membrane / Golgi membrane / endoplasmic reticulum ...inositol phosphorylceramide synthase / mannosyl diphosphorylinositol ceramide metabolic process / inositol phosphoceramide synthase activity / inositol phosphoceramide synthase complex / inositol phosphoceramide synthase regulator activity / inositol phosphoceramide metabolic process / sphingolipid biosynthetic process / Golgi cisterna membrane / Golgi membrane / endoplasmic reticulum / Golgi apparatus / cytoplasm
Similarity search - Function
Inositolphosphorylceramide synthase subunit Kei1 / Inositolphosphotransferase Aur1/Ipt1 / : / Inositolphosphorylceramide synthase subunit Kei1 / PAP2 superfamily / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
Chem-46E / TETRADECANE / Inositol phosphorylceramide synthase catalytic subunit AUR1 / Inositol phosphorylceramide synthase regulatory subunit KEI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsChen, J.H. / Ke, Y. / Zhang, M. / Yu, H.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2026
Title: Molecular insights into fungal inositol phosphorylceramide synthesis and its inhibition by antifungal aureobasidin A.
Authors: Jiehui Chen / Yan Ke / Min Zhang / Xinyuan Lin / Zhengkang Hua / Di Zhang / Xinlin Hu / Xuyang Ding / Jiameng Li / Ping Yang / Hongjun Yu /
Abstract: Fungal inositol phosphorylceramide (IPC) synthase is an essential enzyme complex that catalyzes a critical step in sphingolipid biosynthesis. It is the molecular target of potent antifungal ...Fungal inositol phosphorylceramide (IPC) synthase is an essential enzyme complex that catalyzes a critical step in sphingolipid biosynthesis. It is the molecular target of potent antifungal aureobasidin A (AbA). Despite its therapeutic relevance, the lack of structural and mechanistic insights into IPC synthase function and inhibition has impeded rational antifungal drug development. Here, we present cryo-EM structures of Saccharomyces cerevisiae IPC synthase in two distinct functional states: a ceramide-bound form and an AbA-inhibited complex. Our study reveals a conserved heterodimeric architecture formed by Aur1 and Kei1, stabilized through extensive protein-protein and lipid-mediated interactions. Within catalytic Aur1, we identify a membrane-embedded reaction chamber harboring a conserved H-H-D catalytic triad (H255, H294, and D298) essential for IPC synthesis. Structural comparisons illuminate the mechanism of ceramide recognition and reveal how AbA acts as a competitive inhibitor by occupying the substrate-binding pocket. Further analyses identify key residues involved in AbA binding and explain the molecular basis of drug resistance. Together, these findings advance the mechanistic understanding of fungal IPC biosynthesis and inhibition, and establish a foundation for developing new antifungal drugs targeting IPC synthase.
History
DepositionOct 26, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol phosphorylceramide synthase catalytic subunit AUR1
B: Inositol phosphorylceramide synthase regulatory subunit KEI1
C: Aureobasidin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8816
Polymers71,8483
Non-polymers1,0333
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

#1: Protein Inositol phosphorylceramide synthase catalytic subunit AUR1 / IPC synthase catalytic subunit AUR1 / Aureobasidin A resistance protein / Phosphatidylinositol: ...IPC synthase catalytic subunit AUR1 / Aureobasidin A resistance protein / Phosphatidylinositol:ceramide phosphoinositol transferase


Mass: 45223.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: AUR1, YKL004W / Production host: Homo sapiens (human)
References: UniProt: P36107, inositol phosphorylceramide synthase
#2: Protein Inositol phosphorylceramide synthase regulatory subunit KEI1 / ICP synthase regulatory subunit KEI1 / KEX2-cleavable protein essential for inositol ...ICP synthase regulatory subunit KEI1 / KEX2-cleavable protein essential for inositol phosphorylceramide synthesis


Mass: 25505.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: KEI1, YDR367W / Production host: Homo sapiens (human) / References: UniProt: Q06346
#3: Protein/peptide Aureobasidin-A


Mass: 1119.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-C14 / TETRADECANE


Mass: 198.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30
#5: Chemical ChemComp-46E / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate


Mass: 635.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H66NO8P
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: Membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.071 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS TALOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19.1_4122model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228212 / Symmetry type: POINT
RefinementHighest resolution: 3.53 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033916
ELECTRON MICROSCOPYf_angle_d0.7045336
ELECTRON MICROSCOPYf_dihedral_angle_d5.41539
ELECTRON MICROSCOPYf_chiral_restr0.049587
ELECTRON MICROSCOPYf_plane_restr0.004628

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