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- EMDB-61050: Cryo-EM structure of hOAT1 in complex with glibenclamide -

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Basic information

Entry
Database: EMDB / ID: EMD-61050
TitleCryo-EM structure of hOAT1 in complex with glibenclamide
Map data
Sample
  • Complex: Cryo-EM structure of hOAT1 in complex with glibenclamide
    • Protein or peptide: Solute carrier family 22 member 6
  • Ligand: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
Keywordstransporter / Organic Anion / uptake / renal pathophysiology / TRANSPORT PROTEIN
Function / homology
Function and homology information


renal tubular secretion / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / Organic anion transport by SLC22 transporters / sodium-independent organic anion transport / : / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity / solute:inorganic anion antiporter activity ...renal tubular secretion / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / Organic anion transport by SLC22 transporters / sodium-independent organic anion transport / : / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity / solute:inorganic anion antiporter activity / organic anion transport / : / monoatomic anion transport / chloride ion binding / antiporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / basal plasma membrane / caveola / basolateral plasma membrane / protein-containing complex / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Organic cation transport protein/SVOP / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 22 member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsYang DX / Luo YB / Wu XN
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
Other governmentZYYC21006
Other government2022YFC2303700
CitationJournal: Sci Adv / Year: 2025
Title: Structures and membrane interactions of human OAT1 in complex with clinical used drugs.
Authors: Xuening Wu / Yongbo Luo / Shijian Feng / Haiyun Ma / Bowen Ke / Kunjie Wang / Zhaoming Su / Dongxue Yang /
Abstract: Organic anion transporters (OATs) in mammals mediate the renal excretion of numerous structurally diverse organic anionic compounds. Therapeutically inhibiting OATs has emerged as a strategy to ...Organic anion transporters (OATs) in mammals mediate the renal excretion of numerous structurally diverse organic anionic compounds. Therapeutically inhibiting OATs has emerged as a strategy to modulate the elimination or retention of these substrates. Among them, OAT1 plays a pivotal role in the pharmacokinetics and drug-drug interactions of a wide range of prescription medications. Despite extensive structural investigations, the molecular structure, and basis of polyspecific anionic drug recognition of human OAT1 (hOAT1) have remained elusive. Here, we present cryogenic electron microscopy structures of hOAT1 and its complexes with the antiviral drug cidofovir and an FDA-approved type II diabetes medication glibenclamide, respectively. Our findings reveal that both cidofovir and glibenclamide bind to a central binding site, capturing the transporter in inward-facing conformations. These structures elucidate how specific residues within the central site orchestrate the binding of chemically diverse inhibitors and provide a structural basis for the drug recognition mechanism of hOAT1.
History
DepositionAug 2, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61050.png

Downloads & links

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Map

FileDownload / File: emd_61050.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.165
Minimum - Maximum-0.6747397 - 1.117984
Average (Standard dev.)0.00075485586 (±0.025215786)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61050_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_61050_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of hOAT1 in complex with glibenclamide

EntireName: Cryo-EM structure of hOAT1 in complex with glibenclamide
Components
  • Complex: Cryo-EM structure of hOAT1 in complex with glibenclamide
    • Protein or peptide: Solute carrier family 22 member 6
  • Ligand: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide

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Supramolecule #1: Cryo-EM structure of hOAT1 in complex with glibenclamide

SupramoleculeName: Cryo-EM structure of hOAT1 in complex with glibenclamide
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 6

MacromoleculeName: Solute carrier family 22 member 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.869027 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFNDLLQQV GGVGRFQQIQ VTLVVLPLLL MASHNTLQNF TAAIPTHHCR PPADANLSKN GGLEVWLPRD RQGQPESCLR FTSPQWGLP FLNGTEANGT GATEPCTDGW IYDNSTFPST IVTEWDLVCS HRALRQLAQS LYMVGVLLGA MVFGYLADRL G RRKVLILN ...String:
MAFNDLLQQV GGVGRFQQIQ VTLVVLPLLL MASHNTLQNF TAAIPTHHCR PPADANLSKN GGLEVWLPRD RQGQPESCLR FTSPQWGLP FLNGTEANGT GATEPCTDGW IYDNSTFPST IVTEWDLVCS HRALRQLAQS LYMVGVLLGA MVFGYLADRL G RRKVLILN YLQTAVSGTC AAFAPNFPIY CAFRLLSGMA LAGISLNCMT LNVEWMPIHT RACVGTLIGY VYSLGQFLLA GV AYAVPHW RHLQLLVSAP FFAFFIYSWF FIESARWHSS SGRLDLTLRA LQRVARINGK REEGAKLSME VLRASLQKEL TMG KGQASA MELLRCPTLR HLFLCLSMLW FATSFAYYGL VMDLQGFGVS IYLIQVIFGA VDLPAKLVGF LVINSLGRRP AQMA ALLLA GICILLNGVI PQDQSIVRTS LAVLGKGCLA ASFNCIFLYT GELYPTMIRQ TGMGMGSTMA RVGSIVSPLV SMTAE LYPS MPLFIYGAVP VAASAVTVLL PETLGQPLPD TVQDLESRWA PTQKEAGIYP RKGKQTRQQQ EHQKYMVPLQ ASAQEK NGL

UniProtKB: Solute carrier family 22 member 6

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Macromolecule #2: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-...

MacromoleculeName: 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
type: ligand / ID: 2 / Number of copies: 1 / Formula: GBM
Molecular weightTheoretical: 494.004 Da
Chemical component information

ChemComp-GBM:
5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / medication*YM

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.841 µm / Nominal defocus min: 0.617 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152395
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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