Our laboratory has isolated and continues to study the cytochrome c
oxidase of Neurospora crassa. It is our experience that subunit 1 of
the oxidase aggregates when it is boiled in SDS sample buffer in
preparation for electrophoresis. Instead, we add SDS sample buffer to
the proteins, leave at room temperature for 1 hr, followed by 4oC
overnight. You might try this protocol before electrophoresis to see
if the "contaminant" disappears. Good luck.