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- PDB-9vpg: Cryo-EM structure of human urate transporter GLUT9 bound to a sel... -

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Basic information

Entry
Database: PDB / ID: 9vpg
TitleCryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
ComponentsSolute carrier family 2, facilitated glucose transporter member 9
KeywordsTRANSPORT PROTEIN / complex / selective inhibitor
Function / homology
Function and homology information


Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) / fructose transmembrane transporter activity / fructose transmembrane transport / dehydroascorbic acid transport / hexose transmembrane transport / carbohydrate:proton symporter activity / Cellular hexose transport / D-glucose transmembrane transporter activity / D-glucose transmembrane transport / urate transport ...Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) / fructose transmembrane transporter activity / fructose transmembrane transport / dehydroascorbic acid transport / hexose transmembrane transport / carbohydrate:proton symporter activity / Cellular hexose transport / D-glucose transmembrane transporter activity / D-glucose transmembrane transport / urate transport / urate metabolic process / urate transmembrane transporter activity / : / transmembrane transporter activity / basolateral plasma membrane / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Glucose transporter GLUT / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
: / Solute carrier family 2, facilitated glucose transporter member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsPan, X. / Shen, Z. / Luo, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32322039 China
CitationJournal: Acta Pharm Sin B / Year: 2026
Title: Selective GLUT9 inhibitors for hyperuricemia via intestinal mechanism
Authors: Zhao, Z. / Sun, Z. / Shen, Z. / Zheng, F. / Zhang, X. / Luo, Z. / He, Y. / Xu, Y. / Wu, Z. / Ke, J. / Li, J. / Wu, T. / Zhang, Q. / Tian, Y. / Pan, X. / Pang, J. / Chen, J.
History
DepositionJul 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 2, facilitated glucose transporter member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5642
Polymers63,2151
Non-polymers3491
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 Solute carrier family 2, facilitated glucose transporter member 9 / Glucose transporter type 9 / GLUT-9 / Urate transporter


Mass: 63215.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A9, GLUT9 / Production host: Homo sapiens (human) / References: UniProt: Q9NRM0
#2: Chemical ChemComp-A1ETZ / (~{E})-3-[2-(4-hydroxyphenyl)-4-oxidanylidene-3~{H}-quinazolin-8-yl]-~{N}-propan-2-yl-prop-2-enamide


Mass: 349.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
7UCSF ChimeraXmodel fitting
9Cootmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36474 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8Y65

8y65


Accession code: 8Y65 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033687
ELECTRON MICROSCOPYf_angle_d0.5585024
ELECTRON MICROSCOPYf_dihedral_angle_d11.876521
ELECTRON MICROSCOPYf_chiral_restr0.038590
ELECTRON MICROSCOPYf_plane_restr0.004633

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