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- EMDB-65253: Cryo-EM structure of human urate transporter GLUT9 bound to a sel... -

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Basic information

Entry
Database: EMDB / ID: EMD-65253
TitleCryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
Map data
Sample
  • Complex: Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 9
  • Ligand: (~{E})-3-[2-(4-hydroxyphenyl)-4-oxidanylidene-3~{H}-quinazolin-8-yl]-~{N}-propan-2-yl-prop-2-enamide
Keywordscomplex / selective inhibitor / transport protein
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsPan X / Shen Z / Luo Z
Funding support China, 1 items
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, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65253.png

Downloads & links

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Map

FileDownload / File: emd_65253.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 192 pix.
= 210.797 Å		1.1 Å/pix.
x 192 pix.
= 210.797 Å		1.1 Å/pix.
x 192 pix.
= 210.797 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.597
Minimum - Maximum-2.027751 - 3.2542934
Average (Standard dev.)0.0075246063 (±0.08131553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 210.79681 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65253_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65253_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human urate transporter GLUT9 bound to a sel...

EntireName: Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
Components
  • Complex: Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
    • Protein or peptide: Solute carrier family 2, facilitated glucose transporter member 9
  • Ligand: (~{E})-3-[2-(4-hydroxyphenyl)-4-oxidanylidene-3~{H}-quinazolin-8-yl]-~{N}-propan-2-yl-prop-2-enamide

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Supramolecule #1: Cryo-EM structure of human urate transporter GLUT9 bound to a sel...

SupramoleculeName: Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 63.21509 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTARKQNRN SKELGLVPLT DDTSHAGPPG PGRALLECDH LRSGVPGGR RRKDWSCSLL VASLAGAFGS SFLYGYNLSV VNAPTPYIKA FYNESWERRH GRPIDPDTLT LLWSVTVSIF A IGGLVGTL ...String:
MASWSHPQFE KGGGARGGSG GGSWSHPQFE KGFDYKDDDD KGTARKQNRN SKELGLVPLT DDTSHAGPPG PGRALLECDH LRSGVPGGR RRKDWSCSLL VASLAGAFGS SFLYGYNLSV VNAPTPYIKA FYNESWERRH GRPIDPDTLT LLWSVTVSIF A IGGLVGTL IVKMIGKVLG RKHTLLANNG FAISAALLMA CSLQAGAFEM LIVGRFIMGI DGGVALSVLP MYLSEISPKE IR GSLGQVT AIFICIGVFT GQLLGLPELL GKESTWPYLF GVIVVPAVVQ LLSLPFLPDS PRYLLLEKHN EARAVKAFQT FLG KADVSQ EVEEVLAESR VQRSIRLVSV LELLRAPYVR WQVVTVIVTM ACYQLCGLNA IWFYTNSIFG KAGIPPAKIP YVTL STGGI ETLAAVFSGL VIEHLGRRPL LIGGFGLMGL FFGTLTITLT LQDHAPWVPY LSIVGILAII ASFCSGPGGI PFILT GEFF QQSQRPAAFI IAGTVNWLSN FAVGLLFPFI QKSLDTYCFL VFATICITGA IYLYFVLPET KNRTYAEISQ AFSKRN KAY PPEEKIDSAV TDGKINGRP

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

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Macromolecule #2: (~{E})-3-[2-(4-hydroxyphenyl)-4-oxidanylidene-3~{H}-quinazolin-8-...

MacromoleculeName: (~{E})-3-[2-(4-hydroxyphenyl)-4-oxidanylidene-3~{H}-quinazolin-8-yl]-~{N}-propan-2-yl-prop-2-enamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1ETZ
Molecular weightTheoretical: 349.383 Da

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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: 6
GridModel: Quantifoil / Material: GOLD / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8y65

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36474
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8y65


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9vpg:
Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4

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