The succinate dehydrogenase complex (complex II) is a highly conserved protein complex composed of the SDH1 to SDH4 subunits in bacteria and in the mitochondria of animals and fungi. The reason for the occurrence of up to four additional subunits in complex II of plants, termed SDH5 to SDH8, so far is a mystery. Here, we present a biochemical approach to investigate the internal subunit arrangement of Arabidopsis (Arabidopsis thaliana) complex II. Using low-concentration detergent treatments, the holo complex is dissected into subcomplexes that are analyzed by a three-dimensional gel electrophoresis system. Protein identifications by mass spectrometry revealed that the largest subcomplex (IIa) represents the succinate dehydrogenase domain composed of SDH1 and SDH2. Another subcomplex (IIb) is composed of the SDH3, SDH4, SDH6, and SDH7 subunits. All four proteins include transmembrane helices and together form the membrane anchor of complex II. Sequence analysis revealed that SDH3 and SDH4 lack helices conserved in other organisms. Using homology modeling and phylogenetic analyses, we present evidence that SDH6 and SDH7 substitute missing sequence stretches of SDH3 and SDH4 in plants. Together with SDH5, which is liberated upon dissection of complex II into subcomplexes, SDH6 and SDH7 also add some hydrophilic mass to plant complex II, which possibly inserts further functions into this smallest protein complex of the oxidative phosphorylation system (which is not so small in plants).Succinate dehydrogenase (EC 1.3.5.1) is of central importance for energy metabolism in bacteria and mitochondria of eukaryotic cells. In mitochondria, it represents the complex II of the oxidative phosphorylation (OXPHOS) system (Hatefi, 1985) and is located in the inner mitochondrial membrane. Complex II participates in two major mitochondrial processes: the tricarboxylic acid cycle as well as the mitochondrial electron transfer chain (mETC). In the tricarboxylic acid cycle, it catalyzes the conversion of succinate into fumarate. Electrons originating from this reaction are inserted into the mETC and used for the reduction of ubiquinone to ubiquinol. In contrast to other protein complexes of the OXPHOS system, complex II does not contribute to the proton gradient across the inner mitochondrial membrane.The overall structure of the succinate dehydrogenase complex is remarkably conserved in bacteria, animals, and fungi, as revealed by biochemical investigations and x-ray crystallography (Yankovskaya et al., 2003;Oyedotun and Lemire, 2004;Sun et al., 2005;Huang et al., 2006;Iverson, 2013). It is about 120 kD in size and composed of four subunits designated SDH1, SDH2, SDH3, and SDH4 (also named SDHA to SDHD in some bacteria). SDH1 is the largest subunit and includes the succinate-binding site. Electrons from succinate are accepted by a covalently bound FAD group. SDH2 carries three iron-sulfur clusters that mediate electron transfer from SDH1 to the membrane domain of complex II. Together with SDH1, it constitutes the succinate dehydrog...