8BVT

Cryo-EM structure of rat SLC22A6 bound to probenecid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1.

Parker, J.L.Kato, T.Kuteyi, G.Sitsel, O.Newstead, S.

(2023) Nat Struct Mol Biol 30: 1786-1793

  • DOI: https://doi.org/10.1038/s41594-023-01039-y
  • Primary Citation of Related Structures:  
    8BVR, 8BVS, 8BVT, 8BW7, 8OMU

  • PubMed Abstract: 

    In mammals, the kidney plays an essential role in maintaining blood homeostasis through the selective uptake, retention or elimination of toxins, drugs and metabolites. Organic anion transporters (OATs) are responsible for the recognition of metabolites and toxins in the nephron and their eventual urinary excretion. Inhibition of OATs is used therapeutically to improve drug efficacy and reduce nephrotoxicity. The founding member of the renal organic anion transporter family, OAT1 (also known as SLC22A6), uses the export of α-ketoglutarate (α-KG), a key intermediate in the Krebs cycle, to drive selective transport and is allosterically regulated by intracellular chloride. However, the mechanisms linking metabolite cycling, drug transport and intracellular chloride remain obscure. Here, we present cryogenic-electron microscopy structures of OAT1 bound to α-KG, the antiviral tenofovir and clinical inhibitor probenecid, used in the treatment of Gout. Complementary in vivo cellular assays explain the molecular basis for α-KG driven drug elimination and the allosteric regulation of organic anion transport in the kidney by chloride.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford, UK. joanne.parker@bioch.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 22 member 6547Rattus nativitatisMutation(s): 0 
Gene Names: Slc22a6Oat1
Membrane Entity: Yes 
UniProt
Find proteins for O35956 (Rattus norvegicus)
Explore O35956 
Go to UniProtKB:  O35956
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35956
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Synthetic nanobody (Sybody)146synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RTO (Subject of Investigation/LOI)
Query on RTO

Download Ideal Coordinates CCD File 
C [auth A]4-(dipropylsulfamoyl)benzoic acid
C13 H19 N O4 S
DBABZHXKTCFAPX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom215519
Wellcome TrustUnited Kingdom219531
Medical Research Council (MRC, United Kingdom)United KingdomMR/S021043/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-19
    Type: Initial release
  • Version 1.1: 2023-08-02
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references