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- PDB-8zxm: Cryo-EM structure of human GLUT9 bound to urate -

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Basic information

Entry
Database: PDB / ID: 8zxm
TitleCryo-EM structure of human GLUT9 bound to urate
ComponentsSolute carrier family 2, facilitated glucose transporter member 9
KeywordsTRANSPORT PROTEIN / Urate / Transporter / Hypouricemia / RHUC
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 / D-glucose import / 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
URIC ACID / Solute carrier family 2, facilitated glucose transporter member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsMatsushita, D. / Lee, Y. / Nishizawa, T.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K18064 Japan
Japan Society for the Promotion of Science (JSPS)23K27132 Japan
Japan Society for the Promotion of Science (JSPS)24H02264 Japan
Japan Science and TechnologyJPMJPR21EF Japan
Japan Society for the Promotion of Science (JSPS)21K15031 Japan
Japan Society for the Promotion of Science (JSPS)20H03216 Japan
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis of urate transport by glucose transporter 9.
Authors: Daiki Matsushita / Yu Toyoda / Yongchan Lee / Maeda Aoi / Hirotaka Matsuo / Tappei Takada / Tomohiro Nishizawa /
Abstract: Glucose transporter 9 (GLUT9) is a critical urate transporter involved in renal reabsorption, playing a pivotal role in regulating physiological urate levels and representing a potential therapeutic ...Glucose transporter 9 (GLUT9) is a critical urate transporter involved in renal reabsorption, playing a pivotal role in regulating physiological urate levels and representing a potential therapeutic target for gout. Despite such clinical significance, the structural basis of urate recognition and transport by GLUT9 remains elusive. Here, we present the cryoelectron microscopy (cryo-EM) structures of GLUT9 in the inward-open conformation in both apo and urate-bound states. Urate binds in a cleft between the N-terminal and C-terminal domains, interacting via hydrogen bonds and hydrophobic interactions. Structural comparison with sugar-transporting GLUTs highlights unique amino acid compositions in the substrate recognition pocket of GLUT9. Functional and mutational studies directly measuring GLUT9-mediated urate uptake further demonstrate the cooperative roles of multiple residues in urate recognition. Our findings elucidate the structural basis of urate transport by GLUT9 and provide valuable insights for the development of uricosuric drugs targeting GLUT9.
History
DepositionJun 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: 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)60,3003
Polymers59,7071
Non-polymers5932
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: 59707.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC2A9, GLUT9 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q9NRM0
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3 / 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: Glucose transporter 9 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 60 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 180531 / Symmetry type: POINT
RefinementResolution: 3.39→3.39 Å / Cor.coef. Fo:Fc: 0.79 / SU B: 16.093 / SU ML: 0.253 / ESU R: 0.695
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.42055 --
obs0.42055 29278 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 127.209 Å2
Refinement stepCycle: 1 / Total: 3666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0113762
ELECTRON MICROSCOPYr_bond_other_d00.0163675
ELECTRON MICROSCOPYr_angle_refined_deg1.5251.6375132
ELECTRON MICROSCOPYr_angle_other_deg0.4911.5558432
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.4465470
ELECTRON MICROSCOPYr_dihedral_angle_2_deg3.429518
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.52610594
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0820.2606
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.024323
ELECTRON MICROSCOPYr_gen_planes_other0.0010.02875
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it14.66711.1351883
ELECTRON MICROSCOPYr_mcbond_other14.66611.1361883
ELECTRON MICROSCOPYr_mcangle_it21.98720.1762352
ELECTRON MICROSCOPYr_mcangle_other21.98720.1882353
ELECTRON MICROSCOPYr_scbond_it19.47913.9611879
ELECTRON MICROSCOPYr_scbond_other19.47513.9611879
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other30.35524.5572781
ELECTRON MICROSCOPYr_long_range_B_refined36.197139.5814951
ELECTRON MICROSCOPYr_long_range_B_other36.197139.5814952
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.365 2178 -
obs--100 %

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