HMN 2026: How Cryoelectron tomography reveals paracrystalline architecture of proteasome storage granules

Cells organize their molecules into distinct functional areas. While textbooks usually refer to membrane-bound organelles such as mitochondria and cell nuclei, recent studies have also revealed organelles without membranes. These include stress granules and proteasome storage granules (PSGs).

In the past, these membraneless organelles were only visible as “droplets” using a fluorescence microscope. Now, researchers from the Max Planck Institute of Biochemistry in Martinsried, University Medical Center Göttingen, and University of Toronto have defined the detailed structures of molecules in PSGs for the first time, using cryoelectron tomography.

The results are published in the journal Cell.

A proteasome is a large protein complex that works as an energy-powered “protein shredder,” eliminating specific unneeded or damaged proteins by chopping them into small pieces. Proteasomes are found in all eukaryotes, from yeast to humans, and are essential for life.

Proteasomes are also essential for tumor cells to respond to some anti-cancer drugs. When certain nutrients or other sources of cellular energy are too low, the locations of proteasomes inside cells are visibly altered. As key executioners of cellular well-being and functions, proteasomes are a critical focus of research.

Professor Brenda Schulman, Director of the Max Planck Institute (MPI) of Biochemistry, explains, “Thanks to the collaboration with the pioneer in the field of cryoelectron tomography, Professor Wolfgang Baumeister, we are now able to understand how proteasome storage granules function at the molecular level. We knew that many molecular machines assemble into membrane-less organelles, but to truly understand their function, we needed to see their molecular structure.”

Paracrystalline structure of proteasome storage granules

Dr. Cordula Enenkel, an expert in PSG research who works with structural biologist Prof. Oliver Ernst at the University of Toronto, explains, “We subjected yeast cells to energy stress by depriving them of glucose or blocking mitochondrial ATP production. This created ATP—the cells’ energy source—scarcity. In response, the cells shut down their energy-intensive proteasomes by arranging them into PSGs.”

Ernst adds, “We recognized that visualizing the structures of proteasome storage granules would be crucial to understanding this fascinating cellular strategy to cope with metabolic stress, but this was not possible with purified proteasomes.”

Dr. Xiaomeng Tang, one of the first authors of the study from the MPI of Biochemistry and the University Medical Center Göttingen (UMG), explains, “We studied the proteasome storage granules in their natural environment—inside cells. Cryo-electron tomography (ET) enabled us to view the PSGs with a resolution of 0.9 nanometers, revealing structural details that were previously impossible to see. We saw for the first time that individual proteasomes become arranged into precise, repetitive structures like crystals. This was very informative, because what we saw contradicted expectations that PSGs would assemble into amorphous clusters or dynamic liquid droplets.”

The team deciphered the detailed assembly of the PSGs.

“The proteasomes first form trimers. This means that three proteasomes bind together. This has never been observed in cells before,” Tang continues. “These trimers then stack up to form fibers. The fibers bind together to form bundles.”

Cryo-electron tomography as a key technology

Co-first author Dr. Lu Qu from the MPI of Biochemistry and the UMG explains, “We were only able to demonstrate this proteasome arrangement within cells, but not in test tubes. When we tried to isolate the PSGs, the structures disintegrated—that’s why cryoelectron tomography was essential.”

In yeast cells, the PSGs remain fully assembled but inactive, so they do not burn energy during energy shortages.

Qu adds, “The proteasomes are kept in an inactive state by specific protein-protein interactions. The resulting paracrystalline assembly is stable, but it can also be shattered. This allows rapid reactivation of the fully-assembled proteasomes as soon as a source of energy becomes available. When the researchers supplied glucose to the starved cells, the proteasomes returned to their normal functioning structures within an hour.”

A paradigm shift: A membraneless organelle where structure determines function

Prof. Schulman explains, “The discovery provides a new view of membraneless organelle formation through contacts between well-structured regions of molecular machines. This allows PSGs to safely store proteasomes—which are energetically costly to make, and essential—in reserve, ready for deployment when cellular conditions improve.”

Prof. Baumeister summarizes, “Studying structures inside of cells—like proteasomes in their native environment—fundamentally changes our understanding of cellular organization and function.”

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