Do Jin Kim
Structural biologist, now at Denali Therapeutics, who worked in James Hurley's lab at UC Berkeley on the protein machines of autophagy and on the Rag-Ragulator complex that brings mTORC1 to the lysosome
Denali Therapeutics, South San Francisco (Hurley lab alumni list) · Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley (Hurley lab, papers 2014–2019)
Portrait: LinkedIn
Do Jin Kim is a co-author of three Berkeley papers in this Atlas that describe, in atomic detail, the docking station for mTORC1, the growth-control complex, on the lysosome. SUX2017 combined several structural methods into a 'hybrid' model of the RagA/C-Ragulator complex, the scaffold that holds the Rag GTPases on the lysosome surface. LAW2018 found that nutrients change how tightly the Rag GTPases bind their lysosomal scaffold, Ragulator, a switch that controls whether mTORC1 is pulled to the lysosome. LAW2019 solved the structure of the folliculin complex, FLCN with its partner FNIP2, bound to the Rag GTPases and Ragulator on the lysosome. Folliculin acts as a checkpoint that switches on one of the Rag proteins, RagC, which mTORC1 needs to be recruited. Loss of FLCN causes Birt-Hogg-Dubé syndrome, an inherited condition with kidney tumours.
Structures like these explain how a nutrient signal is turned into a physical change in proteins, and they show where drugs might act. They come from purified proteins and cells, not from animals.
Kim's earlier papers with Hurley's group, from 2014 and 2015, mapped the protein complexes that start autophagy: the Atg1/ULK1 complex, the autophagy PI3-kinase complex and the Atg13-Atg101 pair. The Hurley lab's alumni list now places Kim at Denali Therapeutics, a biotechnology company in South San Francisco. It does not give a job title.
Milestones in the Atlas
A selection, not a full bibliography: only papers that meet the Atlas inclusion criteria.
| Year | Evidence | Study |
|---|---|---|
| 2017 | M | Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex SUX2017 Co-author of the hybrid structural model of the RagA/C-Ragulator complex. |
| 2018 | M | A nutrient-induced affinity switch controls mTORC1 activation by its Rag GTPase-Ragulator lysosomal scaffold LAW2018 Co-author of the study showing that nutrients flip an affinity switch between the Rag GTPases and Ragulator. |
| 2019 | M | Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex LAW2019 Co-author of the structural study showing the folliculin complex as a checkpoint for Rag GTPase activation. |
Co-authors in the Atlas 7
People with a profile here who share at least one study with Do Jin Kim.
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- James H. Hurley 3 shared studies Structural biologist who uses cryo-EM to show how protein machines assembled on membranes control autophagy and nutrient signalling. His lab solved structures of the Rag–Ragulator complex and of the whole mTORC1–TFEB–Rag–Ragulator assembly on the lysosome
- Roberto Zoncu 3 shared studies Showed as a postdoc that mTORC1 senses amino acids from inside the lysosome, through the v-ATPase and Ragulator. His Berkeley lab has since mapped how the Rag GTPases and the folliculin complex switch mTORC1 on, and how lysosomal cholesterol feeds into the same system
- Rosalie E. Lawrence 2 shared studies Working in Roberto Zoncu's lab, uncovered the nutrient-driven affinity switch and the FLCN checkpoint that gate mTORC1 activation at the lysosome
- Ashley M. Thelen Cell biologist who did graduate work in Roberto Zoncu's lysosome lab at UC Berkeley, first author of a 2017 review on the lysosome's roles in lipid metabolism, and later a postdoctoral scholar in Philip Greenberg's lab at Fred Hutch
- Chun-Yan Lim Cell biologist who trained in Roberto Zoncu's lab at UC Berkeley on how cholesterol controls mTORC1, and now publishes as corresponding author from Guangzhou National Laboratory on lysosome signalling in immunity and nutrient sensing
- Ming-Yuan Su Structural biologist who solved cryo-EM structures of lysosomal complexes in James Hurley's lab at UC Berkeley and now leads cryo-EM studies of mTORC1 regulators as corresponding author at the Southern University of Science and Technology in Shenzhen
- Ofer Moldavski Researcher who worked on lysosomes and lipid signalling in Roberto Zoncu's lab at UC Berkeley and was first author of a 2021 study on how the oxysterol 4beta-hydroxycholesterol switches on fat-making genes
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