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Yorodumi- EMDB-38966: Cryo-EM structure of human urate transporter GLUT9 bound to subst... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38966 | |||||||||
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Title | Cryo-EM structure of human urate transporter GLUT9 bound to substrate urate | |||||||||
Map data | Cryo-EM structure of human urate transporter GLUT9 bound to substrate urate in detergent micelles | |||||||||
Sample |
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Keywords | GLUT9 / Urate / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) / fructose transmembrane transporter activity / hexose transmembrane transporter activity / monosaccharide transmembrane transport / fructose transmembrane transport / hexose transmembrane transport / carbohydrate:proton symporter activity / Cellular hexose transport / glucose transmembrane transporter activity / urate transport ...Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) / fructose transmembrane transporter activity / hexose transmembrane transporter activity / monosaccharide transmembrane transport / fructose transmembrane transport / hexose transmembrane transport / carbohydrate:proton symporter activity / Cellular hexose transport / glucose transmembrane transporter activity / urate transport / urate metabolic process / glucose transmembrane transport / urate transmembrane transporter activity / transmembrane transporter activity / basolateral plasma membrane / apical plasma membrane / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.51 Å | |||||||||
Authors | Pan XJ / Shen ZL / Xu L / Huang GXY | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis for urate recognition and apigenin inhibition of human GLUT9. Authors: Zilin Shen / Li Xu / Tong Wu / Huan Wang / Qifan Wang / Xiaofei Ge / Fang Kong / Gaoxingyu Huang / Xiaojing Pan / 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, ...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. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38966.map.gz | 25.4 MB | EMDB map data format | |
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Header (meta data) | emd-38966-v30.xml emd-38966.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38966_fsc.xml | 6.9 KB | Display | FSC data file |
Images | emd_38966.png | 155.8 KB | ||
Filedesc metadata | emd-38966.cif.gz | 5.5 KB | ||
Others | emd_38966_half_map_1.map.gz emd_38966_half_map_2.map.gz | 25 MB 25 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38966 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38966 | HTTPS FTP |
-Validation report
Summary document | emd_38966_validation.pdf.gz | 696.5 KB | Display | EMDB validaton report |
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Full document | emd_38966_full_validation.pdf.gz | 696.1 KB | Display | |
Data in XML | emd_38966_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_38966_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38966 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38966 | HTTPS FTP |
-Related structure data
Related structure data | 8y65MC 8y66C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38966.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of human urate transporter GLUT9 bound to substrate urate in detergent micelles | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.0979 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38966_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38966_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GLUT9 in complex with urate
Entire | Name: GLUT9 in complex with urate |
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Components |
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-Supramolecule #1: GLUT9 in complex with urate
Supramolecule | Name: GLUT9 in complex with urate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Solute carrier family 2, facilitated glucose transporter member 9
Macromolecule | Name: Solute carrier family 2, facilitated glucose transporter member 9 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 63.21509 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: URIC ACID
Macromolecule | Name: URIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: URC |
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Molecular weight | Theoretical: 168.11 Da |
Chemical component information | ChemComp-URC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 6 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.56 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |