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- EMDB-60544: Cryo-EM structure of human GLUT9 bound to urate -

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Basic information

Entry
Database: EMDB / ID: EMD-60544
TitleCryo-EM structure of human GLUT9 bound to urate
Map datasharpened map
Sample
  • Complex: Glucose transporter 9
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 9
  • Ligand: URIC ACID
KeywordsUrate / Transporter / Hypouricemia / RHUC / TRANSPORT PROTEIN
Function / homology
Function and homology information


Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) / monosaccharide transmembrane transport / fructose transmembrane transporter activity / hexose transmembrane transporter activity / fructose transmembrane transport / hexose transmembrane transport / carbohydrate:proton symporter activity / Cellular hexose transport / D-glucose transmembrane transporter activity / D-glucose transmembrane transport ...Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) / monosaccharide transmembrane transport / fructose transmembrane transporter activity / hexose transmembrane transporter activity / fructose transmembrane 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsMatsushita D / Lee Y / Nishizawa T
Funding support Japan, 6 items
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, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60544.png

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Map

FileDownload / File: emd_60544.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 160 pix.
= 212.48 Å		1.33 Å/pix.
x 160 pix.
= 212.48 Å		1.33 Å/pix.
x 160 pix.
= 212.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.328 Å
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Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.5361595 - 4.5536423
Average (Standard dev.)0.0005764512 (±0.09897278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_60544_msk_1.map
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Mask #2

Fileemd_60544_msk_2.map
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Half map: map half A

Fileemd_60544_half_map_1.map
Annotationmap half A
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Half map: map half B

Fileemd_60544_half_map_2.map
Annotationmap half B
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Sample components

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Entire : Glucose transporter 9

EntireName: Glucose transporter 9
Components
  • Complex: Glucose transporter 9
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 9
  • Ligand: URIC ACID

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Supramolecule #1: Glucose transporter 9

SupramoleculeName: Glucose transporter 9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60 kDa/nm

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Macromolecule #1: Solute carrier family 2, facilitated glucose transporter member 9

MacromoleculeName: Solute carrier family 2, facilitated glucose transporter member 9
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.707477 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARKQNRNSK ELGLVPLTDD TSHAGPPGPG RALLECDHLR SGVPGGRRRK DWSCSLLVAS LAGAFGSSFL YGYNLSVVNA PTPYIKAFY NESWERRHGR PIDPDTLTLL WSVTVSIFAI GGLVGTLIVK MIGKVLGRKH TLLANNGFAI SAALLMACSL Q AGAFEMLI ...String:
MARKQNRNSK ELGLVPLTDD TSHAGPPGPG RALLECDHLR SGVPGGRRRK DWSCSLLVAS LAGAFGSSFL YGYNLSVVNA PTPYIKAFY NESWERRHGR PIDPDTLTLL WSVTVSIFAI GGLVGTLIVK MIGKVLGRKH TLLANNGFAI SAALLMACSL Q AGAFEMLI VGRFIMGIDG GVALSVLPMY LSEISPKEIR GSLGQVTAIF ICIGVFTGQL LGLPELLGKE STWPYLFGVI VV PAVVQLL SLPFLPDSPR YLLLEKHNEA RAVKAFQTFL GKADVSQEVE EVLAESRVQR SIRLVSVLEL LRAPYVRWQV VTV IVTMAC YQLCGLNAIW FYTNSIFGKA GIPPAKIPYV TLSTGGIETL AAVFSGLVIE HLGRRPLLIG GFGLMGLFFG TLTI TLTLQ DHAPWVPYLS IVGILAIIAS FCSGPGGIPF ILTGEFFQQS QRPAAFIIAG TVNWLSNFAV GLLFPFIQKS LDTYC FLVF ATICITGAIY LYFVLPETKN RTYAEISQAF SKRNKAYPPE EKIDSAVTDG KINGRPGTEN LYFQ

UniProtKB: Solute carrier family 2, facilitated glucose transporter member 9

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Macromolecule #3: URIC ACID

MacromoleculeName: URIC ACID / type: ligand / ID: 3 / Number of copies: 1 / Formula: URC
Molecular weightTheoretical: 168.11 Da
Chemical component information

ChemComp-URC:
URIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180531
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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