Callegari S, Kirk NS, Gan ZY, Dite T, Cobbold SA, Leis A, Dagley LF, Glukhova A, Komander D. Structure of human PINK1 at a mitochondrial TOM-VDAC array. https://doi.org/10.1126/science.adu6445
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Callegari S, Kirk NS, Gan ZY, Dite T, Cobbold SA, Leis A, Dagley LF, Glukhova A, Komander D. Structure of human PINK1 at a mitochondrial TOM-VDAC array. https://doi.org/10.1126/science.adu6445
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MRC Protein Phosphorylation and Ubiquitylation Unit
More than a decade ago, Youle, Lazarou, and Matsuda first showed biochemically that human PINK1 is stabilized on the mitochondrial TOM complex. Since then, there has been great interest in understanding the mechanism. This new cryo-EM structure represents a remarkable advance in our understanding of how human PINK1 is stabilized at the TOM complex, and Komander and his team deserve high praise for this work. Consistent with recent biochemical studies, including from our lab, the structure explains how TOM20 stabilizes PINK1 at the complex. But the structure also provides unprecedented new insights about a role for TOM5 in stabilizing PINK1, and about how the N-terminus of PINK1 traverses the TOM40 pore.
This complements a parallel analysis we have undertaken, in which we performed TurboID proximity labelling proteomics of endogenous PINK1 in human cells, observing robust interaction with TOM5, TOM40, and other components (manuscript under preparation). The discovery that PINK1-TOM complex is assembled with VDAC2 is intriguing and raises several important questions, including how ubiquitylation of VDAC2 by Parkin would affect the complex and the ensuant activation of PINK1.
Overall, the PINK1 structure opens many new avenues for investigation and will be a valuable resource for companies developing activators.
View all comments by Miratul MuqitNational Institutes of Health
Mitochondria produce energy for our cells but are also prone to damage. How does the cell know when a mitochondrion is damaged? One way is through the PINK1-Parkin mitophagy pathway, with PINK1 serving as the damage sensor (reviewed in Narendra and Youle, 2024). PINK1 is targeted to all mitochondria but quickly removed from the surface of healthy mitochondria. In damaged mitochondria, however, PINK1 becomes stuck in the entrance, trapped between the import gates of the outer (TOM complex) and inner (TIM23 complex) mitochondrial membranes. PINK1 so trapped accumulates on the surface, where it activates Parkin to mark the damaged mitochondrion for lysosomal clearance. This cleanup pathway is especially important in long-lived cells like neurons. Indeed, loss of either PINK1 or Parkin function causes Parkinson’s disease.
Although this damage sensing mechanism has been known for over a decade, it had never been seen up close. That is, until this remarkable new article from Sylvie Callegari, Alisa Glukhova, David Komander, and others, in which they provide the first clear view of PINK1 stuck in the import path of a damaged mitochondrion. The structure is stunning. A pair of PINK1 molecules, each sitting in a separate TOM complex, reach across the pore of VDAC2 to make contact.
Many features of the structure are surprising and will certainly reshape how we understand damage sensing by PINK1 as well as mitochondrial import more generally. Perhaps most surprisingly was the presence of a VDAC2 dimer between the PINK1 dimer. Together with the two TOM complex dimers this formed a striking array of six beta-barrel proteins, altogether forming six pores in the outer mitochondrial membrane (OMM), only two of which were occupied by PINK1.
Also surprising were the specific subunits of the TOM complex that were found to hold PINK1 to the surface. These included not only those long implicated in PINK1 stabilization on the OMM, such as the import receptor TOMM20, and the small subunit TOMM7, but also the small subunit TOMM5. In a recent preprint from my lab, we showed TOMM5 to be required for PINK1 stabilization on the OMM, providing functional validation of this structural observation (Thayer et al., 2025). The structure was also notable for what was absent: namely, another import receptor called TOMM70. TOMM70 has been proposed to be important for PINK1 stabilization on the OMM in some contexts, such as in vitro import assays, and when reconstituting PINK1 stabilization on the OMM in yeast (Raimi et al., 2024; Maruszczak et al., 2022; Kato et al., 2013). Consistent with its absence in this structure, however, it was recently shown not to be required for endogenous PINK1 stabilization or import in human cells (Thayer et al., 2025).
The structure also leaves many questions for future work. Perhaps most tantalizing, PINK1 in the dimer appears to be caught near the end of its brief embrace, during which each molecule phosphorylates the other to complete folding of its substrate binding site. Surprisingly, a disulfide bond links the two in this conformation and presumably must be broken to separate them and free each PINK1 molecule to activate Parkin. How does this happen? Is it a regulated process and, if so, what factor regulates it? And why does it happen? Does it serve as a sort of timer, lending PINK1 the buffer period it needs to mature? As the authors tease at the end of their article, there are more structures to come, and, I suspect, more answers.
References:
Narendra DP, Youle RJ. The role of PINK1-Parkin in mitochondrial quality control. Nat Cell Biol. 2024 Oct;26(10):1639-1651. Epub 2024 Oct 2 PubMed.
Thayer JA, Petersen JD, Huang X, Hawrot J, Ramos DM, Sekine S, Li Y, Ward ME, Narendra DP. Novel reporter of the PINK1-Parkin mitophagy pathway identifies its damage sensor in the import gate. bioRxiv. 2025 Feb 20; PubMed.
Raimi OG, Ojha H, Ehses K, Dederer V, Lange SM, Rivera CP, Deegan TD, Chen Y, Wightman M, Toth R, Labib KP, Mathea S, Ranson N, Fernández-Busnadiego R, Muqit MM. Mechanism of human PINK1 activation at the TOM complex in a reconstituted system. Sci Adv. 2024 Jun 7;10(23):eadn7191. PubMed.
Maruszczak KK, Jung M, Rasool S, Trempe JF, Rapaport D. The role of the individual TOM subunits in the association of PINK1 with depolarized mitochondria. J Mol Med (Berl). 2022 May;100(5):747-762. Epub 2022 Apr 7 PubMed.
Kato H, Lu Q, Rapaport D, Kozjak-Pavlovic V. Tom70 is essential for PINK1 import into mitochondria. PLoS One. 2013;8(3):e58435. Epub 2013 Mar 5 PubMed.
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