Molecular basis of mitochondrial leucine transport by human Sideroflexin 1

Leucine is a central nutrient signal and a ketogenic amino acid that fuels metabolism, yet how it is imported into mitochondria remains incompletely defined. Sideroflexins are conserved inner mitochondrial membrane proteins implicated in amino acid transport, but their mechanism and substrate specificity remain unclear. Using cryogenic electron microscopy, we determined the structure of SFXN1 in its matrix-open conformation. AlphaFold and Boltz co-folding of SFXN1 with a library of human metabolites identified leucine as a candidate substrate, findings supported by thermal stability measurements and mitochondrial transport assays. Comparison with a cytoplasmic-open-model reveals an alternating-access “toggle-switch” mechanism of transport. Together, these findings uncover the molecular basis of leucine transport by SFXN1 and provide a framework for understanding its role in metabolism and disease.