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- EMDB-65102: Structure of a membrane-bound inositol phosphorylceramide synthas... -

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Basic information

Entry
Database: EMDB / ID: EMD-65102
TitleStructure of a membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
Map data
Sample
  • Complex: Membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
    • Protein or peptide: Inositol phosphorylceramide synthase catalytic subunit AUR1
    • Protein or peptide: Inositol phosphorylceramide synthase regulatory subunit KEI1
  • Ligand: TETRADECANE
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
Keywordsmembrane 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 / Golgi apparatus ...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 / Golgi apparatus / endoplasmic reticulum / 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 (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen JH / Ke Y / Zhang M / Yu HJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of a membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
Authors: Chen JH / Ke Y / Zhang M
History
DepositionJun 19, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65102.png

Downloads & links

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Map

FileDownload / File: emd_65102.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 288 pix.
= 213.12 Å		0.74 Å/pix.
x 288 pix.
= 213.12 Å		0.74 Å/pix.
x 288 pix.
= 213.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.3811 - 1.6710756
Average (Standard dev.)0.00010478183 (±0.034004144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 213.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65102_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65102_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-bound inositol phosphorylceramide synthase and Aureobasi...

EntireName: Membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
Components
  • Complex: Membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
    • Protein or peptide: Inositol phosphorylceramide synthase catalytic subunit AUR1
    • Protein or peptide: Inositol phosphorylceramide synthase regulatory subunit KEI1
  • Ligand: TETRADECANE
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate

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Supramolecule #1: Membrane-bound inositol phosphorylceramide synthase and Aureobasi...

SupramoleculeName: Membrane-bound inositol phosphorylceramide synthase and Aureobasidin A complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 71 KDa

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Macromolecule #1: Inositol phosphorylceramide synthase catalytic subunit AUR1

MacromoleculeName: Inositol phosphorylceramide synthase catalytic subunit AUR1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: inositol phosphorylceramide synthase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 45.223023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MANPFSRWFL SERPPNCHVA DLETSLDPHQ TLLKVQKYKP ALSDWVHYIF LGSIMLFVFI TNPAPWIFKI LFYCFLGTLF IIPATSQFF FNALPILTWV ALYFTSSYFP DDRRPPITVK VLPAVETILY GDNLSDILAT STNSFLDILA WLPYGLFHFG A PFVVAAIL ...String:
MANPFSRWFL SERPPNCHVA DLETSLDPHQ TLLKVQKYKP ALSDWVHYIF LGSIMLFVFI TNPAPWIFKI LFYCFLGTLF IIPATSQFF FNALPILTWV ALYFTSSYFP DDRRPPITVK VLPAVETILY GDNLSDILAT STNSFLDILA WLPYGLFHFG A PFVVAAIL FVFGPPTVLQ GYAFAFGYMN LFGVIMQNVF PAAPPWYKIL YGLQSANYDM HGSPGGLARI DKLLGINMYT TA FSNSSVI FGAFPSLHSG CATMEALFFC YCFPKLKPLF IAYVCWLWWS TMYLTHHYFV DLMAGSVLSY VIFQYTKYTH LPI VDTSLF CRWSYTSIEK YDISKSDPLA ADSNDIESVP LSNLELDFDL NMTDEPSVSP SLFDGSTSVS RSSATSITSL GVKR A

UniProtKB: Inositol phosphorylceramide synthase catalytic subunit AUR1

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Macromolecule #2: Inositol phosphorylceramide synthase regulatory subunit KEI1

MacromoleculeName: Inositol phosphorylceramide synthase regulatory subunit KEI1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 25.505799 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRSSLLTLPK SFLGFMPLYL AVEIVLGISI LNKCSGAYGI LALFTGHPLD FMQWIAYLWS VFTLIVFSQG LYLIHKPNLL VFSQICVLY TIDTISTCFF TLWFTTQWFT LEDTANIDGN NALQSNPIST GKLTERGIDI SKQSATESYE YTMTILITLV S LIFRFYFN ...String:
MRSSLLTLPK SFLGFMPLYL AVEIVLGISI LNKCSGAYGI LALFTGHPLD FMQWIAYLWS VFTLIVFSQG LYLIHKPNLL VFSQICVLY TIDTISTCFF TLWFTTQWFT LEDTANIDGN NALQSNPIST GKLTERGIDI SKQSATESYE YTMTILITLV S LIFRFYFN FILASFVQEL LHHPKYLVDR DDVEQNLKNK PIWKRLWAKS QKGCYKLCKN LLE

UniProtKB: Inositol phosphorylceramide synthase regulatory subunit KEI1

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Macromolecule #3: TETRADECANE

MacromoleculeName: TETRADECANE / type: ligand / ID: 3 / Number of copies: 2 / Formula: C14
Molecular weightTheoretical: 198.388 Da
Chemical component information

ChemComp-C14:
TETRADECANE

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Macromolecule #4: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...

MacromoleculeName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate
type: ligand / ID: 4 / Number of copies: 1 / Formula: 46E
Molecular weightTheoretical: 635.853 Da
Chemical component information

ChemComp-46E:
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl tetradecanoate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TALOS
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: 3.0 µm / Nominal defocus min: 1.1 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 226357
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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