MitoAtlas: a Domain-Resolved Spatial Map of the HumanMitochondrial Proteome

Kang, J.; Shin, S.; Kwak, C.; Lee, S.-Y.; Jung, M.; Lee, H.; Kang, M.-G.; Sim, J.; Lee, S.-J. V.; Mun, J. Y.; Kim, J.-S.; Rhee, H.-W.

doi:10.64898/2026.04.03.716438

bioRxiv · 10.64898/2026.04.03.716438

MitoAtlas: a Domain-Resolved Spatial Map of the HumanMitochondrial Proteome

Kang, J.·Shin, S.·Kwak, C.·Lee, S.-Y.·Jung, M.·Lee, H.·Kang, M.-G.·Sim, J.·Lee, S.-J. V.·Mun, J. Y.·Kim, J.-S.·Rhee, H.-W.

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Abstract

Mitochondrial function depends on the precise sub-organellar localization and topological orientation of its proteome. However, mapping this architecture with domain-level precision across the double-membrane system has remained challenging. Here, we present MitoAtlas, a spatial systems biology resource built on SR-PL (super-resolution proximity labeling) that resolves the sub-mitochondrial architecture of 861 proteins at domain-level resolution. By deploying 42 spatially restricted APEX2 and BioID/BioID2 baits across mitochondrial compartments and cytosol in HEK293T-REx cells, we mapped 13,440 unique proximity-labeled sites. Integrating high-density spatial data with a machine-learning classification pipeline and AlphaFold structural modeling, we resolved membrane topologies for 196 transmembrane proteins and assigned sub-mitochondrial localizations to 160 previously unannotated mitochondrial proteins absent from MitoCarta3.0, including MINPP1 as an intermembrane space resident. Coupling bait-specific proximity labeling signatures with AlphaFold structure prediction and metabolite docking identified 47 protein-protein interactions, including the LETM1-Citrate Synthase complex, and 155 protein-metabolite interactions. MitoAtlas is available at mitoatlas.org as a domain-resolution spatial map of mitochondrial architecture and metabolism.

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Kang, J., Shin, S., Kwak, C., Lee, S.-Y., Jung, M., Lee, H., Kang, M.-G., Sim, J., Lee, S.-J. V., Mun, J. Y., Kim, J.-S., Rhee, H.-W.. 2026-04-05. MitoAtlas: a Domain-Resolved Spatial Map of the HumanMitochondrial Proteome. https://doi.org/10.64898/2026.04.03.716438

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