9IVC | pdb_00009ivc

Cryo-EM structure of AbA-bound Aur1-Kei1 complex

• PDB DOI: https://doi.org/10.2210/pdb9IVC/pdb
• EM Map EMD-60924: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C, Aureobasidium pullulans
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-07-23 Released: 2025-06-18 
• Deposition Author(s): Xie, T., Wu, X., Gong, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanisms of aureobasidin A inhibition and drug resistance in a fungal IPC synthase complex.

Wu, X., Gong, X., Xie, T.

(2025) Nat Commun 16: 5010-5010

• PubMed: 40442105 
• DOI: https://doi.org/10.1038/s41467-025-60423-y
• Primary Citation Related Structures: 
  9IVC


• PubMed 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. 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.

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Organizational Affiliation: 
• Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China. [e-mail].
Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China. [e-mail].
Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China. [e-mail].
Shenzhen Key Laboratory of Plant Genetic Engineering and Molecular Design, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China. [e-mail].
Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B2C1D1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 157.71 kDa 
• Atom Count: 8,632 
• Modeled Residue Count: 1,062 
• Deposited Residue Count: 1,400 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol phosphorylceramide synthase catalytic subunit AUR1	A, C	449	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: AUR1, YKL004W EC: 2.7.1.227 Membrane Entity: Yes
UniProt
Find proteins for P36107 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36107  Go to UniProtKB:  P36107

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol phosphorylceramide synthase regulatory subunit KEI1	B, D	242	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: KEI1, YDR367W Membrane Entity: Yes
UniProt
Find proteins for Q06346 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q06346  Go to UniProtKB:  Q06346

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Aureobasidin A	E, F	9	Aureobasidium pullulans	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1L3I	E, F	L-PEPTIDE LINKING	C6 H13 N O3		--
IIL	E, F	L-PEPTIDE LINKING	C6 H13 N O2		ILE
MEA	E, F	L-PEPTIDE LINKING	C10 H13 N O2		PHE
MVA	E, F	L-PEPTIDE LINKING	C6 H13 N O2		VAL

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Xie, T., Wu, X., Gong, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release