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- EMDB-80824: Cryo-EM structure of human UGCG bound to UDP and C6-ceramide -

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Basic information

Entry
Database: EMDB / ID: EMD-80824
TitleCryo-EM structure of human UGCG bound to UDP and C6-ceramide
Map data
Sample
  • Complex: human UGCG bound to UDP and C6-ceramide
    • Protein or peptide: Ceramide glucosyltransferase
  • Ligand: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE
  • Ligand: URIDINE-5'-DIPHOSPHATE
KeywordsCeramide glucosyltransferase / UGCG / GCS / TRANSFERASE
Function / homology
Function and homology information


ceramide glucosyltransferase / glucosylceramide biosynthetic process / ceramide glucosyltransferase activity / Glycosphingolipid biosynthesis / cornified envelope assembly / protein lipidation / intestinal lipid absorption / leptin-mediated signaling pathway / glycosphingolipid biosynthetic process / epidermis development ...ceramide glucosyltransferase / glucosylceramide biosynthetic process / ceramide glucosyltransferase activity / Glycosphingolipid biosynthesis / cornified envelope assembly / protein lipidation / intestinal lipid absorption / leptin-mediated signaling pathway / glycosphingolipid biosynthetic process / epidermis development / keratinocyte differentiation / establishment of skin barrier / neuron development / regulation of signal transduction / cell differentiation / Golgi membrane / membrane
Similarity search - Function
Ceramide glucosyltransferase / Glycosyl transferase family 21 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Ceramide glucosyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWu C / Jin S / Xu J / Wang JJ / Guo X / Li Y / Cao Z / Jiang M / Yuan Q / Hu W ...Wu C / Jin S / Xu J / Wang JJ / Guo X / Li Y / Cao Z / Jiang M / Yuan Q / Hu W / Li C / Xu Y / Wang MW / Jiang Y / Xu HE
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2026
Title: Primate-specific regulation of the human glycosphingolipid gatekeeper UGCG
Authors: Wu C / Jin S / Xu J / Wang JJ / Guo X / Li Y / Cao Z / Jiang M / Yuan Q / Hu W / Li C / Xu Y / Wang MW / Jiang Y / Xu HE
History
DepositionMay 11, 2026-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80824.png

Downloads & links

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Map

FileDownload / File: emd_80824.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.)
0.73 Å/pix.
x 288 pix.
= 210.24 Å		0.73 Å/pix.
x 288 pix.
= 210.24 Å		0.73 Å/pix.
x 288 pix.
= 210.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.686
Minimum - Maximum-3.1879303 - 4.6138225
Average (Standard dev.)0.0004520124 (±0.08319365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 210.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_80824_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_80824_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 : human UGCG bound to UDP and C6-ceramide

EntireName: human UGCG bound to UDP and C6-ceramide
Components
  • Complex: human UGCG bound to UDP and C6-ceramide
    • Protein or peptide: Ceramide glucosyltransferase
  • Ligand: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE
  • Ligand: URIDINE-5'-DIPHOSPHATE

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Supramolecule #1: human UGCG bound to UDP and C6-ceramide

SupramoleculeName: human UGCG bound to UDP and C6-ceramide / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ceramide glucosyltransferase

MacromoleculeName: Ceramide glucosyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ceramide glucosyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.899562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALLDLALEG MAVFGFVLFL VLWLMHFMAI IYTRLHLNKK ATDKQPYSKL PGVSLLKPLK GVDPNLINNL ETFFELDYPK YEVLLCVQD HDDPAIDVCK KLLGKYPNVD ARLFIGGKKV GINPKINNLM PGYEVAKYDL IWICDSGIRV IPDTLTDMVN Q MTEKVGLV ...String:
MALLDLALEG MAVFGFVLFL VLWLMHFMAI IYTRLHLNKK ATDKQPYSKL PGVSLLKPLK GVDPNLINNL ETFFELDYPK YEVLLCVQD HDDPAIDVCK KLLGKYPNVD ARLFIGGKKV GINPKINNLM PGYEVAKYDL IWICDSGIRV IPDTLTDMVN Q MTEKVGLV HGLPYVADRQ GFAATLEQVY FGTSHPRYYI SANVTGFKCV TGMSCLMRKD VLDQAGGLIA FAQYIAEDYF MA KAIADRG WRFAMSTQVA MQNSGSYSIS QFQSRMIRWT KLRINMLPAT IICEPISECF VASLIIGWAA HHVFRWDIMV FFM CHCLAW FIFDYIQLRG VQGGTLCFSK LDYAVAWFIR ESMTIYIFLS ALWDPTISWR TGRYRLRCGG TAEEILDV

UniProtKB: Ceramide glucosyltransferase

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Macromolecule #2: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE

MacromoleculeName: N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE
type: ligand / ID: 2 / Number of copies: 1 / Formula: 6CM
Molecular weightTheoretical: 397.635 Da
Chemical component information

ChemComp-6CM:
N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE

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Macromolecule #3: URIDINE-5'-DIPHOSPHATE

MacromoleculeName: URIDINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: UDP
Molecular weightTheoretical: 404.161 Da
Chemical component information

ChemComp-UDP:
URIDINE-5'-DIPHOSPHATE / UDP*YM

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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

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 155359
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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