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- PDB-26qf: Cryo-EM structure of human Ceramide glucosyltransferase UGCG -

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Basic information

Entry
Database: PDB / ID: 26qf
TitleCryo-EM structure of human Ceramide glucosyltransferase UGCG
ComponentsCeramide glucosyltransferase
KeywordsTRANSFERASE / Ceramide glucosyltransferase
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsWu, C. / Jin, S. / Xu, J. / Wang, J.J. / Guo, X. / Li, Y. / Cao, Z. / Jiang, M. / Yuan, Q. / Hu, W. ...Wu, C. / Jin, S. / Xu, J. / Wang, J.J. / Guo, X. / Li, Y. / Cao, Z. / Jiang, M. / Yuan, Q. / Hu, W. / Li, C. / Xu, Y. / Wang, M.W. / Jiang, Y. / Xu, H.E.
Funding support China, 1items
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, J.J. / Guo, X. / Li, Y. / Cao, Z. / Jiang, M. / Yuan, Q. / Hu, W. / Li, C. / Xu, Y. / Wang, M.W. / Jiang, Y. / Xu, H.E.
History
DepositionMay 11, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ceramide glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)44,9001
Polymers44,9001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Ceramide glucosyltransferase / GLCT-1 / Glucosylceramide synthase / GCS / Glycosylceramide synthase / UDP-glucose ceramide ...GLCT-1 / Glucosylceramide synthase / GCS / Glycosylceramide synthase / UDP-glucose ceramide glucosyltransferase / UDP-glucose:N-acylsphingosine D-glucosyltransferase


Mass: 44899.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGCG / Production host: Homo sapiens (human) / References: UniProt: Q16739, ceramide glucosyltransferase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ceramide glucosyltransferase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4particle selection
2PHENIX1.17.1_3660model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46441 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0013112
ELECTRON MICROSCOPYf_angle_d0.3874220
ELECTRON MICROSCOPYf_dihedral_angle_d17.989411
ELECTRON MICROSCOPYf_chiral_restr0.037466
ELECTRON MICROSCOPYf_plane_restr0.003522

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