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- EMDB-46951: Structure of URAT1 in complex with TD-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-46951
TitleStructure of URAT1 in complex with TD-3
Map datafull map
Sample
  • Complex: URAT1
    • Protein or peptide: URAT1
  • Ligand: 2-({1-[(4-bromonaphthalen-1-yl)methyl]-1H-imidazo[4,5-b]pyridin-2-yl}sulfanyl)-2-methylpropanoic acid
KeywordsMembrane protein / membrane transporter / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsSuo Y / Fedor JG / Lee S-Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2025
Title: Molecular basis of the urate transporter URAT1 inhibition by gout drugs.
Authors: Suo Y / Fedor JG / Zhang H / Tsolova K / Shi X / Sharma K / Kumari S / Borgnia M / Zhan P / Im W / Lee SY
History
DepositionSep 8, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_46951.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Voxel sizeX=Y=Z: 0.8469 Å
Density
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.758975 - 5.2521615
Average (Standard dev.)0.003637623 (±0.114852265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 216.8064 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : URAT1

EntireName: URAT1
Components
  • Complex: URAT1
    • Protein or peptide: URAT1
  • Ligand: 2-({1-[(4-bromonaphthalen-1-yl)methyl]-1H-imidazo[4,5-b]pyridin-2-yl}sulfanyl)-2-methylpropanoic acid

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Supramolecule #1: URAT1

SupramoleculeName: URAT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55 KDa

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Macromolecule #1: URAT1

MacromoleculeName: URAT1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.379844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFSELLDQV GGLGRFQVLQ TVALVVPIMW LCTQSMLENF SAAVPSHRCW VPLLDNSTAQ ASVPGALGPE ALLAVSIPPG PNQGPHQCR RFRQPQWQLL DPNATATNWS EAATEPCVDG WVYDRSTFTS TIVAKWDLVC DSQALKPMAQ SIYLAGILVG A AVCGPASD ...String:
MAFSELLDQV GGLGRFQVLQ TVALVVPIMW LCTQSMLENF SAAVPSHRCW VPLLDNSTAQ ASVPGALGPE ALLAVSIPPG PNQGPHQCR RFRQPQWQLL DPNATATNWS EAATEPCVDG WVYDRSTFTS TIVAKWDLVC DSQALKPMAQ SIYLAGILVG A AVCGPASD RFGRRLVLTW SYLQMAVSGT AAAFAPTFPV YCLFRFLVAF AVAGVMMNTG TLVMEWTSAQ ARPLVMTLNS LG FSFGHVL MAAVAYGVRD WALLQLVVSV PFFLCFVYSC WLAESARWLL ITGRLDRGLR ELQRVAAING KRAVGDTLTP QVL LSAMQE ELSVGQAPAS LGTLLRTPGL RLRTCISTLC WFAFGFTFFG LALDLQALGS NIFLLQVLIG VVDIPAKIGT LLLL SRLGR RPTQAASLVL AGLCILANTL VPHEMGALRS ALAVLGLGGL GAAFTCITIY SGELFPTVLR MTAVGLGQMA ARGGA ILGP LVRLLGVHGP WLPLLVYGTV PVLSGLAALL LPET

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Macromolecule #2: 2-({1-[(4-bromonaphthalen-1-yl)methyl]-1H-imidazo[4,5-b]pyridin-2...

MacromoleculeName: 2-({1-[(4-bromonaphthalen-1-yl)methyl]-1H-imidazo[4,5-b]pyridin-2-yl}sulfanyl)-2-methylpropanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1A45
Molecular weightTheoretical: 456.356 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

Concentration10 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
150.0 mMNaClNaCl
0.005 %LMNGLMNG
GridModel: Quantifoil R1.2/1.3 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00039000000000000005 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 280 K / Instrument: LEICA EM GP
DetailsMonodisperse sample

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMax: 70.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 18880 / Average exposure time: 1.8 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1954727
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 505707
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.0)

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Atomic model buiding 1

Initial modelPDB ID:

8et6


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 200
Output model

PDB-9dkc:
Structure of URAT1 in complex with TD-3

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