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- EMDB-65613: Cryo-EM structure of the 4:4 Lac1-Lip1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65613
TitleCryo-EM structure of the 4:4 Lac1-Lip1 complex
Map data
Sample
  • Complex: Lac1-Lip1 complex
    • Protein or peptide: Ceramide synthase LAC1
    • Protein or peptide: Ceramide synthase subunit LIP1
KeywordsComplex / Transferase
Function / homology
Function and homology information


very-long-chain ceramide synthase / acyl-CoA ceramide synthase complex / Sphingolipid de novo biosynthesis / sphingosine N-acyltransferase activity / ceramide biosynthetic process / nuclear periphery / nuclear envelope / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
TRAM/LAG1/CLN8 homology domain / Sphingosine N-acyltransferase Lag1/Lac1-like / TLC domain / TLC domain profile. / TRAM, LAG1 and CLN8 homology domains.
Similarity search - Domain/homology
Ceramide synthase LAC1 / Ceramide synthase subunit LIP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsXie T / Gong X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2026
Title: Structural and functional dissection of a higher-order oligomerization interface in yeast ceramide synthase
Authors: Fang Q / Yang C / Yao N / Xie T / Gong X
History
DepositionJul 30, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65613.png

Downloads & links

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Map

FileDownload / File: emd_65613.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 514.56 Å		1.07 Å/pix.
x 480 pix.
= 514.56 Å		1.07 Å/pix.
x 480 pix.
= 514.56 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: 0.4
Minimum - Maximum-2.8881233 - 3.8684905
Average (Standard dev.)-0.0006243666 (±0.045176126)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 514.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #2

Fileemd_65613_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65613_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65613_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lac1-Lip1 complex

EntireName: Lac1-Lip1 complex
Components
  • Complex: Lac1-Lip1 complex
    • Protein or peptide: Ceramide synthase LAC1
    • Protein or peptide: Ceramide synthase subunit LIP1

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Supramolecule #1: Lac1-Lip1 complex

SupramoleculeName: Lac1-Lip1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Ceramide synthase LAC1

MacromoleculeName: Ceramide synthase LAC1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: very-long-chain ceramide synthase
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 50.289082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTIKPSPSN NNLKVRSRPR RKSSIGKIDL GDTVPSLGTM FETKESKTAA KRRMQRLSEA TKNDSDLVKK IWFSFREISY RHAWIAPLM ILIAVYSAYF TSGNTTKTNV LHRFVAVSYQ IGDTNAYGKG INDLCFVFYY MIFFTFLREF LMDVVIRPFA I RLHVTSKH ...String:
MSTIKPSPSN NNLKVRSRPR RKSSIGKIDL GDTVPSLGTM FETKESKTAA KRRMQRLSEA TKNDSDLVKK IWFSFREISY RHAWIAPLM ILIAVYSAYF TSGNTTKTNV LHRFVAVSYQ IGDTNAYGKG INDLCFVFYY MIFFTFLREF LMDVVIRPFA I RLHVTSKH RIKRIMEQMY AIFYTGVSGP FGIYCMYHSD LWFFNTKAMY RTYPDFTNPF LFKVFYLGQA AFWAQQACIL VL QLEKPRK DHNELTFHHI VTLLLIWSSY VFHFTKMGLP IYITMDVSDF LLSFSKTLNY LDSGLAFFSF AIFVVAWIYL RHY INLKIL WSVLTQFRTE GNYVLNFATQ QYKCWISLPI VFVLIGALQL VNLYWLFLIF RVLYRILWRG ILKDDRSDSE SDEE SDESS TTPTDSTPTK KDILEDYKDD DDK

UniProtKB: Ceramide synthase LAC1

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Macromolecule #2: Ceramide synthase subunit LIP1

MacromoleculeName: Ceramide synthase subunit LIP1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 17.228682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MSQPTPIITT KSAAKPKPKI FNLFRVCFIS LLLIAAVEYF KYGTRINYEW FHCTPIKEPQ SGSVIKLWAR GGPSCDKRGE YKTIVKRIT RDYEPNDEHL SFCIIENDNV PPVHYPIHED KGEPGYVAYV GYDTDSELVQ ELCADSTIYH M

UniProtKB: Ceramide synthase subunit LIP1

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8y2n

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 219798
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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