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- PDB-9ivc: Cryo-EM structure of AbA-bound Aur1-Kei1 complex -

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Basic information

Entry
Database: PDB / ID: 9ivc
TitleCryo-EM structure of AbA-bound Aur1-Kei1 complex
Components
  • Aureobasidin A
  • Inositol phosphorylceramide synthase catalytic subunit AUR1
  • Inositol phosphorylceramide synthase regulatory subunit KEI1
KeywordsTRANSFERASE / Inhibitor / Complex
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
Inositol phosphorylceramide synthase catalytic subunit AUR1 / Inositol phosphorylceramide synthase regulatory subunit KEI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Aureobasidium pullulans R106 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsXie, T. / Wu, X. / Gong, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Mechanisms of aureobasidin A inhibition and drug resistance in a fungal IPC synthase complex.
Authors: Xinyue Wu / Xin Gong / Tian Xie /
Abstract: The enzyme inositol phosphorylceramide (IPC) synthase is essential for survival and virulence in fungi, while absent in mammals, thus representing a potential target for antifungal treatments. ...The enzyme inositol phosphorylceramide (IPC) synthase is essential for survival and virulence in fungi, while absent in mammals, thus representing a potential target for antifungal treatments. Aureobasidin A (AbA), a natural cyclic peptide, displays antifungal activity and inhibits IPC synthase, but the precise molecular mechanism remains unclear. Here, we present the cryo-EM structure of the Saccharomyces cerevisiae IPC synthase, composed of catalytic subunit Aur1 and regulatory subunit Kei1, in its AbA-bound state. The complex is resolved as a dimer of Aur1-Kei1 heterodimers, with Aur1 mediating homodimerization. AbA occupies a predominantly hydrophobic pocket in the catalytic core domain of each Aur1 subunit, blocking the entry of both substrates. Mutations conferring AbA resistance cluster near the AbA-binding site, thus interfering with AbA binding. Our study lays a foundation for the development of therapeutic drugs targeting fungal IPC synthase.
History
DepositionJul 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: 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: Inositol phosphorylceramide synthase catalytic subunit AUR1
D: Inositol phosphorylceramide synthase regulatory subunit KEI1
E: Aureobasidin A
F: Aureobasidin A


Theoretical massNumber of molelcules
Total (without water)157,7076
Polymers157,7076
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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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: 49956.934 Da / Num. of mol.: 2
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: 27777.113 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) Aureobasidium pullulans R106 (fungus)
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: Aur1-Kei1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 186487 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0088934
ELECTRON MICROSCOPYf_angle_d1.02712212
ELECTRON MICROSCOPYf_dihedral_angle_d7.691130
ELECTRON MICROSCOPYf_chiral_restr0.0541366
ELECTRON MICROSCOPYf_plane_restr0.0061464

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