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- EMDB-45421: Structure of urate bound human SLC2A9 transporter -

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Basic information

Entry
Database: EMDB / ID: EMD-45421
TitleStructure of urate bound human SLC2A9 transporter
Map dataSharp map obtained from refinement
Sample
  • Complex: Codon optimize SLC2A9 gene was synthesize and cloned in 83 nu yeast expressing vector from GenScript. Protein expressed in yeast cells and purified using Ni-affinity followed by Sizing.
    • Protein or peptide: Soluble cytochrome b562,Solute carrier family 2, facilitated glucose transporter member 9
  • Ligand: URIC ACID
KeywordsTransporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC2A9 causes hypouricemia renal 2 (RHUC2) / fructose transmembrane transporter activity / fructose transmembrane transport / hexose transmembrane transport / dehydroascorbic acid 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 / hexose transmembrane transport / dehydroascorbic acid 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 / electron transport chain / basolateral plasma membrane / periplasmic space / electron transfer activity / apical plasma membrane / iron ion binding / heme binding / 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. / Cytochrome b562 ...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. / Cytochrome b562 / Cytochrome b562 / MFS transporter superfamily / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Solute carrier family 2, facilitated glucose transporter member 9
Similarity search - Component
Biological speciesHomo sapiens (Human) (human) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsKhandelwal NK / Gupta M / Stroud RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structure of urate bound human SLC2A9 transporter
Authors: Khandelwal NK / Stroud RM / Gupta MG
History
DepositionJun 18, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45421.png

Downloads & links

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Map

FileDownload / File: emd_45421.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map obtained from refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 294.804 Å		0.82 Å/pix.
x 360 pix.
= 294.804 Å		0.82 Å/pix.
x 360 pix.
= 294.804 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8189 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.3728203 - 2.2136216
Average (Standard dev.)-0.00017073072 (±0.03881597)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 294.804 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpned map obtained from refinement

Fileemd_45421_additional_1.map
Annotationunsharpned map obtained from refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_45421_half_map_1.map
AnnotationHalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B

Fileemd_45421_half_map_2.map
AnnotationHalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Codon optimize SLC2A9 gene was synthesize and cloned in 83 nu yea...

EntireName: Codon optimize SLC2A9 gene was synthesize and cloned in 83 nu yeast expressing vector from GenScript. Protein expressed in yeast cells and purified using Ni-affinity followed by Sizing.
Components
  • Complex: Codon optimize SLC2A9 gene was synthesize and cloned in 83 nu yeast expressing vector from GenScript. Protein expressed in yeast cells and purified using Ni-affinity followed by Sizing.
    • Protein or peptide: Soluble cytochrome b562,Solute carrier family 2, facilitated glucose transporter member 9
  • Ligand: URIC ACID

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Supramolecule #1: Codon optimize SLC2A9 gene was synthesize and cloned in 83 nu yea...

SupramoleculeName: Codon optimize SLC2A9 gene was synthesize and cloned in 83 nu yeast expressing vector from GenScript. Protein expressed in yeast cells and purified using Ni-affinity followed by Sizing.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Purified protein incubated with 1 mM Urate for 5 min.
Source (natural)Organism: Homo sapiens (Human) (human)
Molecular weightTheoretical: 69.78906 KDa

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Macromolecule #1: Soluble cytochrome b562,Solute carrier family 2, facilitated gluc...

MacromoleculeName: Soluble cytochrome b562,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: 69.859695 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASDYKDDDD KGALEVLFQG PSSPMADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHG FDILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YLSCSLLVAS LAGAFGSSFL YGYNLSVVNA P TPYIKAFY ...String:
MASDYKDDDD KGALEVLFQG PSSPMADLED NWETLNDNLK VIEKADNAAQ VKDALTKMRA AALDAQKATP PKLEDKSPDS PEMKDFRHG FDILVGQIDD ALKLANEGKV KEAQAAAEQL KTTRNAYIQK YLSCSLLVAS LAGAFGSSFL YGYNLSVVNA P TPYIKAFY NESWERRHGR PIDPDTLTLL WSVTVSIFAI GGLVGTLIVK MIGKVLGRKH TLLANNGFAI SAALLMACSL QA GAFEMLI VGRFIMGIDG GVALSVLPMY LSEISPKEIR GSLGQVTAIF ICIGVFTGQL LGLPELLGKE STWPYLFGVI VVP AVVQLL SLPFLPDSPR YLLLEKHNEA RAVKAFQTFL GKADVSQEVE EVLAESRVQR SIRLVSVLEL LRAPYVRWQV VTVI VTMAC YQLCGLNAIW FYTNSIFGKA GIPPAKIPYV TLSTGGIETL AAVFSGLVIE HLGRRPLLIG GFGLMGLFFG TLTIT LTLQ DHAPWVPYLS IVGILAIIAS FCSGPGGIPF ILTGEFFQQS QRPAAFIIAG TVNWLSNFAV GLLFPFIQKS LDTYCF LVF ATICITGAIY LYFVLPETKN RTYAEISQAF SKRNKAYPPE EKIDSAVTDG KINGRPGLVP RGSSAHHHHH HHHHHGA

UniProtKB: Soluble cytochrome b562, Solute carrier family 2, facilitated glucose transporter member 9

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Macromolecule #2: URIC ACID

MacromoleculeName: URIC ACID / type: ligand / ID: 2 / 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

Concentration7 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClSodium Chloride
50.0 mMTris-ClTris

Details: 4 degree cold buffer pH7.5 (300mM NaCl, 50mM Tris and 0.02% GDN)
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.033 kPa / Details: 30 sec glow 30 sec hold at 15mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Detailspurified protein incubated with 1 mM Urate for 5 min.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 10941 / Average exposure time: 2.0 sec. / Average electron dose: 47.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8883188
CTF correctionType: NONE
Startup modelType of model: NONE / Details: Alphafold2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44003
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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