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- EMDB-64463: Structure of human URAT1 bound with sulfinpyrazone -

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Basic information

Entry
Database: EMDB / ID: EMD-64463
TitleStructure of human URAT1 bound with sulfinpyrazone
Map dataSharpened map of human URAT1 supplementary with sulfinpyrazone.
Sample
  • Complex: human urate transporter 1
    • Protein or peptide: Solute carrier family 22 member 12
  • Ligand: Sulfinpyrazone
KeywordsSLC22 / urate / gout / sulfinpyrazone / TRANSPORT PROTEIN
Function / homology
Function and homology information


Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / Organic anion transport by SLC22 transporters / renal urate salt excretion / urate transport / urate metabolic process / urate transmembrane transporter activity / : / cellular homeostasis / monoatomic ion transport / PDZ domain binding ...Defective SLC22A12 causes renal hypouricemia 1 (RHUC1) / Organic anion transport by SLC22 transporters / renal urate salt excretion / urate transport / urate metabolic process / urate transmembrane transporter activity / : / cellular homeostasis / monoatomic ion transport / PDZ domain binding / brush border membrane / cellular response to insulin stimulus / apical plasma membrane / response to xenobiotic stimulus / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 22 member 12
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsWei M / Guo WJ / Chen L
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA0806504 China
National Natural Science Foundation of China (NSFC)32225027 China
CitationJournal: To Be Published
Title: Structure of human URAT1 bound with sulfinpyrazone
Authors: Wei M / Guo WJ / Chen L
History
DepositionMay 1, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64463.png

Downloads & links

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Map

FileDownload / File: emd_64463.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of human URAT1 supplementary with sulfinpyrazone.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å		0.83 Å/pix.
x 360 pix.
= 300.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.844
Minimum - Maximum-5.1587067 - 6.7596116
Average (Standard dev.)-0.00011555125 (±0.07525025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64463_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map of human URAT1 supplementary with sulfinpyrazone.

Fileemd_64463_additional_1.map
AnnotationMap of human URAT1 supplementary with sulfinpyrazone.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of human URAT1 supplementary with sulfinpyrazone.

Fileemd_64463_half_map_1.map
AnnotationHalf map of human URAT1 supplementary with sulfinpyrazone.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of human URAT1 supplementary with sulfinpyrazone.

Fileemd_64463_half_map_2.map
AnnotationHalf map of human URAT1 supplementary with sulfinpyrazone.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human urate transporter 1

EntireName: human urate transporter 1
Components
  • Complex: human urate transporter 1
    • Protein or peptide: Solute carrier family 22 member 12
  • Ligand: Sulfinpyrazone

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Supramolecule #1: human urate transporter 1

SupramoleculeName: human urate transporter 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 22 member 12

MacromoleculeName: Solute carrier family 22 member 12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.546602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFSELLDLV GGLGRFQVLQ TMALMVSIMW LCTQSMLENF SAAVPSHRCW APLLDNSTAQ ASILGSLSPE ALLAISIPPG PNQRPHQCR RFRQPQWQLL DPNATATSWS EADTEPCVDG WVYDRSIFTS TIVAKWNLVC DSHALKPMAQ SIYLAGILVG A AVCGPASD ...String:
MAFSELLDLV GGLGRFQVLQ TMALMVSIMW LCTQSMLENF SAAVPSHRCW APLLDNSTAQ ASILGSLSPE ALLAISIPPG PNQRPHQCR RFRQPQWQLL DPNATATSWS EADTEPCVDG WVYDRSIFTS TIVAKWNLVC DSHALKPMAQ SIYLAGILVG A AVCGPASD RFGRRLVLTW SYLQMAVSGT AAAFAPTFPV YCLFRFLLAF AVAGVMMNTG TLLMEWTSAR ARPLVMTLNS LG FSFGHGL TAAVAYGVRD WTLLQLAVSV PFFLCFLYSW WLAESARWLL TTGRLDRGLQ ELRRVAAING KRAVQDTLTP EVL LSAMRE ELSVGQAPAS LGTLLRTPGL RLRTCISTLC WFAFGFTFFG LALDLQALGS NIFLLQVLIG VVDIPAKMGA LLLL SRLGR RPTLAASLLL AGLCILANTL VPHEMGALRS ALAVLGLGGV GAAFTCITIY SSELFPTVLR MTAVGLGQMA ARGGA ILGP LVRLLGVHGP WLPLLVYGTV PVLSGLAALL LPETQSLPLP DTIQDVQNQA VKKATHGTLG NSVLKSTQF

UniProtKB: Solute carrier family 22 member 12

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Macromolecule #2: Sulfinpyrazone

MacromoleculeName: Sulfinpyrazone / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EAY
Molecular weightTheoretical: 404.482 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196309
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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