Molecule of the Month: Respiratory Supercomplex

Researchers have been wondering for decades if proteins team up into large functional complexes inside cells. Some, such as hypothetical glycosomes that bring together all the glycolytic enzymes, still elude detection. But many have been observed, such as the multisynthetase complex that includes eight aminoacyl-tRNA synthases and huge supercomplexes of photosynthetic reaction centers and antenna proteins. Respiratory supercomplexes are a recent addition to this group. The "respirasome" (PDB entry 5xth) is composed of three membrane-bound members of the electron transport chain: complex I, dimeric complex III, and complex IV. Inside mitochondria, it takes electrons produced by the citric acid cycle (delivered by the carrier molecule NADH) and uses them to create the electrochemical gradient that powers ATP synthase. As described below, other respiratory supercomplexes perform related tasks.

It is still a bit of a mystery why these molecular machines assemble into supercomplexes. The most obvious advantage is that it brings the three close together, so that the little molecules that carry electrons between them, ubiquinone and cytochrome c, don’t have to go far. However, this type of substrate channeling has been difficult to observe in experiments. Intriguingly, researchers have found that the supercomplex reduces production of reactive forms of oxygen, which are generated as a dangerous side product of the normal use of oxygen as the final resting place for the electrons.

Looking more closely at the three complexes in the respirasome, we can get a snapshot of the early evolution of eukaryotic cells. These complexes are composed of dozens of subunits, and a few of them are encoded by the small DNA genome that is found inside mitochondria. The mitochondrial genome is thought to date back to the early days of the formation of eukaryotic cells, when a symbiotic cell took up residence inside another cell, so this may show us what the earliest forms of the complexes looked like. This idea is also supported by comparing the mitochondrial complexes with similar proteins in bacteria. They all share a set of “core” protein subunits, decorated by many “supernumerary” subunits that help customize the function for each cell type. As you might expect, all of the mitochondria-encoded subunits are also core subunits.

In mitochondria, the respiratory complexes are found in many states: as individual complexes and as several different supercomplexes. The supercomplex shown here is composed of only complex III and complex IV, glued together with the small protein SCAF1 (PDB ID 7o37). Since its discovery, researchers have hypothesized that this supercomplex makes complex III more accessible to ubiquinone produced by respiratory complex II, shown here from PDB ID 1zoy. Complex II, or succinate dehydrogenase, works as part of the citric acid cycle but also passes electrons to the electron transport chain.