[English] 日本語
Yorodumi
- EMDB-60924: Cryo-EM structure of AbA-bound Aur1-Kei1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60924
TitleCryo-EM structure of AbA-bound Aur1-Kei1 complex
Map data
Sample
  • Complex: Aur1-Kei1 complex
    • Protein or peptide: Inositol phosphorylceramide synthase catalytic subunit AUR1
    • Protein or peptide: Inositol phosphorylceramide synthase regulatory subunit KEI1
    • Protein or peptide: Aureobasidin A
KeywordsInhibitor / Complex / Transferase
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 (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast) / Aureobasidium pullulans R106 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsXie T / Wu X / Gong X
Funding support China, 1 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60924.png

Downloads & links

-
Map

FileDownload / File: emd_60924.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 343.04 Å		1.07 Å/pix.
x 320 pix.
= 343.04 Å		1.07 Å/pix.
x 320 pix.
= 343.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.072 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.37
Minimum - Maximum-2.518743 - 3.3651314
Average (Standard dev.)-0.0011119796 (±0.06186317)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 343.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_60924_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60924_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Aur1-Kei1 complex

EntireName: Aur1-Kei1 complex
Components
  • Complex: Aur1-Kei1 complex
    • Protein or peptide: Inositol phosphorylceramide synthase catalytic subunit AUR1
    • Protein or peptide: Inositol phosphorylceramide synthase regulatory subunit KEI1
    • Protein or peptide: Aureobasidin A

-
Supramolecule #1: Aur1-Kei1 complex

SupramoleculeName: Aur1-Kei1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

-
Macromolecule #1: Inositol phosphorylceramide synthase catalytic subunit AUR1

MacromoleculeName: Inositol phosphorylceramide synthase catalytic subunit AUR1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: inositol phosphorylceramide synthase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 49.956934 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASGHSAWSH PQFEKGGGSG GGSGGSAWSH PQFEKVGSDE VDAGSSGRMA NPFSRWFLSE RPPNCHVADL ETSLDPHQTL LKVQKYKPA LSDWVHYIFL GSIMLFVFIT NPAPWIFKIL FYCFLGTLFI IPATSQFFFN ALPILTWVAL YFTSSYFPDD R RPPITVKV ...String:
MASGHSAWSH PQFEKGGGSG GGSGGSAWSH PQFEKVGSDE VDAGSSGRMA NPFSRWFLSE RPPNCHVADL ETSLDPHQTL LKVQKYKPA LSDWVHYIFL GSIMLFVFIT NPAPWIFKIL FYCFLGTLFI IPATSQFFFN ALPILTWVAL YFTSSYFPDD R RPPITVKV LPAVETILYG DNLSDILATS TNSFLDILAW LPYGLFHFGA PFVVAAILFV FGPPTVLQGY AFAFGYMNLF GV IMQNVFP AAPPWYKILY GLQSANYDMH GSPGGLARID KLLGINMYTT AFSNSSVIFG AFPSLHSGCA TMEALFFCYC FPK LKPLFI AYVCWLWWST MYLTHHYFVD LMAGSVLSYV IFQYTKYTHL PIVDTSLFCR WSYTSIEKYD ISKSDPLAAD SNDI ESVPL SNLELDFDLN MTDEPSVSPS LFDGSTSVSR SSATSITSLG VKRA

UniProtKB: Inositol phosphorylceramide synthase catalytic subunit AUR1

-
Macromolecule #2: Inositol phosphorylceramide synthase regulatory subunit KEI1

MacromoleculeName: Inositol phosphorylceramide synthase regulatory subunit KEI1
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 27.777113 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADYKDDDDK SGPDEVDASG RMRSSLLTLP KSFLGFMPLY LAVEIVLGIS ILNKCSGAYG ILALFTGHPL DFMQWIAYLW SVFTLIVFS QGLYLIHKPN LLVFSQICVL YTIDTISTCF FTLWFTTQWF TLEDTANIDG NNALQSNPIS TGKLTERGID I SKQSATES ...String:
MADYKDDDDK SGPDEVDASG RMRSSLLTLP KSFLGFMPLY LAVEIVLGIS ILNKCSGAYG ILALFTGHPL DFMQWIAYLW SVFTLIVFS QGLYLIHKPN LLVFSQICVL YTIDTISTCF FTLWFTTQWF TLEDTANIDG NNALQSNPIS TGKLTERGID I SKQSATES YEYTMTILIT LVSLIFRFYF NFILASFVQE LLHHPKYLVD RDDVEQNLKN KPIWKRLWAK SQKGCYKLCK NL LE

UniProtKB: Inositol phosphorylceramide synthase regulatory subunit KEI1

-
Macromolecule #3: Aureobasidin A

MacromoleculeName: Aureobasidin A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Aureobasidium pullulans R106 (fungus)
Molecular weightTheoretical: 1.119435 KDa
SequenceString:
(IIL)(MVA)L(A1L3I)(A1L3J)(MVA)F(MEA)P

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 186487
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more