8Y66

Cryo-EM structure of human urate transporter GLUT9 bound to inhibitor apigenin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for urate recognition and apigenin inhibition of human GLUT9.

Shen, Z.Xu, L.Wu, T.Wang, H.Wang, Q.Ge, X.Kong, F.Huang, G.Pan, X.

(2024) Nat Commun 15: 5039-5039

  • DOI: https://doi.org/10.1038/s41467-024-49420-9
  • Primary Citation of Related Structures:  
    8Y65, 8Y66

  • PubMed Abstract: 

    Urate, the physiological form of uric acid and a potent antioxidant in serum, plays a pivotal role in scavenging reactive oxygen species. Yet excessive accumulation of urate, known as hyperuricemia, is the primary risk factor for the development of gout. The high-capacity urate transporter GLUT9 represents a promising target for gout treatment. Here, we present cryo-electron microscopy structures of human GLUT9 in complex with urate or its inhibitor apigenin at overall resolutions of 3.5 Å and 3.3 Å, respectively. In both structures, GLUT9 exhibits an inward open conformation, wherein the substrate binding pocket faces the intracellular side. These structures unveil the molecular basis for GLUT9's substrate preference of urate over glucose, and show that apigenin acts as a competitive inhibitor by occupying the substrate binding site. Our findings provide critical information for the development of specific inhibitors targeting GLUT9 as potential therapeutics for gout and hyperuricemia.


  • Organizational Affiliation

    Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 2, facilitated glucose transporter member 9582Homo sapiensMutation(s): 0 
Gene Names: SLC2A9GLUT9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NRM0 (Homo sapiens)
Explore Q9NRM0 
Go to UniProtKB:  Q9NRM0
PHAROS:  Q9NRM0
GTEx:  ENSG00000109667 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NRM0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGI (Subject of Investigation/LOI)
Query on AGI

Download Ideal Coordinates CCD File 
B [auth A]5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one
C15 H10 O5
KZNIFHPLKGYRTM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32322039
National Natural Science Foundation of China (NSFC)China32271252

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release