9KKK | pdb_00009kkk

Cryo-EM structure of human SLC22A6 (OAT1) in the apo-state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of human OAT1 reveal drug binding and inhibition mechanisms.

Jeon, H.M.Eun, J.Kim, K.H.Kim, Y.

(2025) Structure 33: 1856-1866.e5

  • DOI: https://doi.org/10.1016/j.str.2025.07.019
  • Primary Citation of Related Structures:  
    9KKK, 9KL5, 9KLZ, 9UNX

  • PubMed Abstract: 

    The organic anion transporter 1 (OAT1) plays a key role in excreting waste from organic drug metabolism and contributes significantly to drug-drug interactions and drug disposition. However, the structural basis of specific substrate and inhibitor transport by human OAT1 (hOAT1) has remained elusive. We determined four cryogenic electron microscopy (cryo-EM) structures of hOAT1 in its inward-facing conformation: the apo form, the substrate (olmesartan)-bound form with different anions, and the inhibitor (probenecid)-bound form. Structural and functional analyses revealed that Ser203 has an auxiliary role in chloride coordination, and it is a critical residue modulating olmesartan transport via chloride ion interactions. Structural comparisons indicate that inhibitors not only compete with substrates, but also obstruct substrate exit and entry from the cytoplasmic side, thereby increasing inhibitor retention. The findings can support drug development by providing insights into substrate recognition and the mechanism by which inhibitors arrest the OAT1 transport cycle.


  • Organizational Affiliation
    • Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 22 member 6563Homo sapiensMutation(s): 0 
Gene Names: SLC22A6OAT1PAHT
UniProt & NIH Common Fund Data Resources
Find proteins for Q4U2R8 (Homo sapiens)
Explore Q4U2R8 
Go to UniProtKB:  Q4U2R8
PHAROS:  Q4U2R8
GTEx:  ENSG00000197901 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4U2R8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.1.4
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2022R1A5A103136112

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Data collection, Database references