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- PDB-9j04: Cryo-EM structure of hOAT1 in complex with cidofovir -

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Basic information

Entry
Database: PDB / ID: 9j04
TitleCryo-EM structure of hOAT1 in complex with cidofovir
ComponentsSolute carrier family 22 member 6
KeywordsTRANSPORT PROTEIN / transporter / Organic Anion / uptake / renal pathophysiology
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
Chem-L8P / Solute carrier family 22 member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsYang, D.X. / Luo, Y.B. / Wu, X.N.
Funding support China, 4items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 22 member 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1482
Polymers61,8691
Non-polymers2791
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 22 member 6 / Organic anion transporter 1 / hOAT1 / PAH transporter / hPAHT / Renal organic anion transporter 1 / hROAT1


Mass: 61869.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC22A6, OAT1, PAHT / Production host: Homo sapiens (human) / References: UniProt: Q4U2R8
#2: Chemical ChemComp-L8P / ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid / Cidofovir


Mass: 279.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N3O6P / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antivirus*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of hOAT1 in complex with cidofovir / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2790 nm / Nominal defocus min: 876 nm
Image recordingElectron dose: 57 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129163 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033871
ELECTRON MICROSCOPYf_angle_d0.5735270
ELECTRON MICROSCOPYf_dihedral_angle_d10.3512282
ELECTRON MICROSCOPYf_chiral_restr0.042614
ELECTRON MICROSCOPYf_plane_restr0.005660

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