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TitleStructural basis of drug recognition by human MATE1 transporter.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 9444, Year 2025
Publish dateOct 27, 2025
AuthorsKsenija Romane / Giulia Peteani / Somnath Mukherjee / Julia Kowal / Lorenzo Rossi / Jingkai Hou / Anthony A Kossiakoff / Thomas Lemmin / Kaspar P Locher /
PubMed AbstractHuman MATE1 (multidrug and toxin extrusion protein 1) is highly expressed in the kidney and liver, where it mediates the final step in the excretion of a broad range of cationic drugs, including the ...Human MATE1 (multidrug and toxin extrusion protein 1) is highly expressed in the kidney and liver, where it mediates the final step in the excretion of a broad range of cationic drugs, including the antidiabetic drug metformin, into the urine and bile. This transport process is essential for drug clearance and also affects therapeutic efficacy. To understand the molecular basis of drug recognition by hMATE1, we determined cryo-electron microscopy structures of the transporter in complex with the substrates 1-methyl-4-phenylpyridinium (MPP) and metformin and with the inhibitor cimetidine. The structures reveal a shared binding site located in a negatively charged pocket in the C-lobe of the protein. We functionally validated key interactions using radioactivity-based cellular uptake assays using hMATE1 mutants. Molecular dynamics simulations provide insights into the different binding modes and dynamic behaviour of the ligands within the pocket. Collectively, these findings define the structural basis of hMATE1 substrate specificity and shed light on its role in drug transport and drug-drug interactions.
External linksNat Commun / PubMed:41145429 / PubMed Central
MethodsEM (single particle)
Resolution2.31 - 3.3 Å
Structure data

53489

9r10

EMDB-53489, PDB-9r10:
Cryo-EM structure of human MATE1 in complex with cimetidine
Method: EM (single particle) / Resolution: 3.3 Å

53506

9r1e

EMDB-53506, PDB-9r1e:
Cryo-EM structure of human MATE1 in complex with MPP
Method: EM (single particle) / Resolution: 3.2 Å

53507

9r1f

EMDB-53507, PDB-9r1f:
Cryo-EM structure of human MATE1 in complex with metformin
Method: EM (single particle) / Resolution: 2.31 Å

53508

9r1g

EMDB-53508, PDB-9r1g:
Cryo-EM structure of human MATE1
Method: EM (single particle) / Resolution: 2.95 Å

Chemicals

ChemComp-CLR:
CHOLESTEROL


ChemComp, No image

ChemComp-SD9:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-WRF:
1-methyl-4-phenylpyridin-1-ium / neurotoxin*YM

ChemComp-MF8:
Metformin / medication, antipsychotic*YM

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsTRANSPORT PROTEIN / SLC47A1 / inhibitor / Fab / multidrug transporter / substrate / ligand / apo

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