[English] 日本語
Yorodumi
- EMDB-45421: Structure of urate bound human SLC2A9 transporter -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / 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 / Cytochrome c/b562 / MFS transporter superfamily
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: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter.
Authors: Nitesh Kumar Khandelwal / Meghna Gupta / Paras Kumar / Sree Ganesh Balasubramani / Ignacia Echeverria / Robert M Stroud /
Abstract: Urate provides ~50% of the reducing potential in human and primate plasma which is key to detoxifying reactive oxygen by-products of cellular metabolism. Urate is the endpoint of purine metabolism in ...Urate provides ~50% of the reducing potential in human and primate plasma which is key to detoxifying reactive oxygen by-products of cellular metabolism. Urate is the endpoint of purine metabolism in primates, and its concentration in plasma is a balance between excretion from kidney and intestine, and subsequent reabsorption in and through cells of kidney proximal tubules to maintain a regulated concentration in plasma. SLC2A9 is the primary transporter that returns urate from the basolateral side of kidney tubule cells back to plasma. A shorter splice variant of SLC2A9 is directed to the apical surface where several transporters recapture urate from the tubule back into cells. Too high a concentration in plasma causes hyperuricemia, is linked to gout, and favors kidney stone formation. To understand the molecular basis of uric acid transport and the role of disease-causing mutations in SLC2A9, we determined structures of human SLC2A9 in its apo form, and its urate-bound form by cryo-EM, at resolution of 3.3 Å and 4.1 Å respectively. Both structures are captured in an inward open conformation. Using the inward-facing structure as a template we modeled the outward-facing conformation to understand the alternating access mechanism. Alternative salt bridge pairs on the cytoplasmic side suggest a mechanism that can balance the energetics of the inward open and outward open states. The location of disease-causing mutants suggests their role in impacting function. Our structures elucidate the molecular basis for urate selectivity and transport and provide a platform for future structure-based drug discovery aimed at reducing plasma urate levels in diseases of hyperuricemia and gout.
History
DepositionJun 18, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45421.png

Downloads & links

-
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 °

-
Supplemental data

-
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)

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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.

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more