26QI | pdb_000026qi

Cryo-EM structure of human UGCG bound to Ibiglustat

• PDB DOI: https://doi.org/10.2210/pdb26QI/pdb
• EM Map EMD-80826: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2026-05-11 Released: 2026-09-02 
• Deposition Author(s): 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 Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Primate-specific regulation of the human glycosphingolipid gatekeeper UGCG.

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.

(2026) Nature 

• PubMed: 42649293 
• DOI: https://doi.org/10.1038/s41586-026-10927-4
• Primary Citation Related Structures: 
  26QF, 26QG, 26QH, 26QI, 26QJ, 26QM, 26QS, 26QT


• PubMed Abstract: 
  

  Glycosphingolipids are essential membrane components that organize lipid microdomains and orchestrate cellular signalling, differentiation and neuronal function ^1-4 . In humans, these functions arise from a repertoire of several hundred glycosphingolipid species generated through stepwise glycan elaboration ^5,6 . Entry into this network is controlled by a single committed reaction catalysed by UDP-glucose ceramide glucosyltransferase (UGCG), the gatekeeper that dictates the scale and composition of glycosphingolipid diversity. Despite its biological and therapeutic importance ^7,8 , its mechanism and regulation have remained unknown. Here we report cryogenic electron microscopy structures of full-length human UGCG in eight functional states at 2.9-3.4 Å resolution. UGCG adopts a previously unrecognized triple-pass transmembrane architecture that anchors a GT-A core at the membrane interface and creates a bipartite active site engaging soluble and membrane-embedded substrates. Contrary to canonical GT-A enzymes, UGCG uses a metal-independent catalytic mechanism driven by an arginine network. We identify a primate-specific steric element that tunes lipid affinity and catalytic turnover, modulating glycosphingolipid entry. Structures with clinically used inhibitors reveal how this architecture governs their potency and selectivity. Together, these findings define the structural and evolutionary logic by which one enzyme controls glycosphingolipid diversity and provide a framework for precision modulation of membrane lipid homeostasis in disease.

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Organizational Affiliation: 
• Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. [e-mail].
Lingang Laboratory, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
Division of Cardiology, Department of Internal Medicine and Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
School of Pharmacy, Nanjing Medical University, Nanjing, China.
State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Fujian, China.
Nanjing University of Chinese Medicine, Nanjing, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
Research Center for Deepsea Bioresources, Sanya, China.
Lingang Laboratory, Shanghai, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Research Center for Medicinal Structural Biology, National Research Center for Translational Medicine at Shanghai, State Key Laboratory of Medical Genomics, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China. [e-mail].
Nanjing University of Chinese Medicine, Nanjing, China. [e-mail].
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 45.29 kDa 
• Atom Count: 3,130 
• Modeled Residue Count: 388 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ceramide glucosyltransferase	A	394	Homo sapiens	Mutation(s): 0  Gene Names: UGCG EC: 2.4.1.80
UniProt & NIH Common Fund Data Resources
Find proteins for Q16739 (Homo sapiens) Explore Q16739  Go to UniProtKB:  Q16739
PHAROS:  Q16739 GTEx:  ENSG00000148154

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KYF (Subject of Investigation/LOI)	B [auth A]	(1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl {2-[2-(4-fluorophenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate C20 H24 F N3 O2 S YFHRCLAKZBDRHN-MRXNPFEDSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.43 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1_3660
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release
  
• Version 1.1: 2026-09-09
  Changes: Data collection, Database references