Cytochrome C Oxydase

Evidence of this symbiotic relationship is found in cytochrome c oxidase. The enzyme from mammals is very complex, composed of 13 separate protein chains (the cow enzyme is shown here, from PDB entry 1oco). Three large chains at the core of the enzyme, colored yellow, orange and red here, perform most of the work. Around this are ten smaller chains, colored in greens and blues.

If we look at the cytochrome c oxidase made by a bacterium, PDB entry 1qle shown here on the right, it is much simpler. It is composed of only four chains. Three are similar to the core chains in our enzyme, colored yellow, orange, and red. One additional small chain can just be seen poking out the bottom here, in blue. Notice how similar this enzyme is to the core of the mammalian enzyme, shown on the left.
This similarity is compelling, but the story is even more interesting. Our mitochondria actually contain all of the machinery needed to build their own proteins--they have DNA, ribosomes, and everything. In our cells, the three core subunits of cytochrome c oxidase are built inside our mitochondria, but the remaining ten small chains are built outside in the cytoplasm and then added to the mitochondria later. So, our mitochondria build a bacteria-like enzyme, which our cells then decorate with other proteins to customize its function.