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- PDB-9j06: Cryo-EM structure of hOAT1 in complex with glibenclamide -

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Basic information

Entry
Database: PDB / ID: 9j06
TitleCryo-EM structure of hOAT1 in complex with glibenclamide
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 / sodium-independent organic anion transport / sodium-independent organic anion transmembrane transporter activity / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity ...: / renal tubular secretion / alpha-ketoglutarate transport / alpha-ketoglutarate transmembrane transporter activity / Organic anion transport / sodium-independent organic anion transport / sodium-independent organic anion transmembrane transporter activity / metanephric proximal tubule development / prostaglandin transport / prostaglandin transmembrane transporter activity / solute:inorganic anion antiporter activity / organic anion transport / organic anion transmembrane transporter activity / monoatomic anion transport / antiporter activity / chloride ion binding / 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-GBM / Solute carrier family 22 member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 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: To be published
Title: Structural basis for recognition of two different drugs by human OAT1
Authors: Wu, X.N. / Luo, Y.B. / Feng, S.J.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 13, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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)62,3632
Polymers61,8691
Non-polymers4941
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-GBM / 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide / Glibenclamide / Glyburide


Mass: 494.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28ClN3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*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 glibenclamide
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: 2841 nm / Nominal defocus min: 617 nm
Image recordingElectron dose: 60 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: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152395 / Symmetry type: POINT

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