Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1

Abstract

Cytochrome c oxidase (complex IV, CIV) is known in mammals to exist independently or in association with other respiratory proteins to form supercomplexes (SCs). In Saccharomyces cerevisiae, CIV is found solely in an SC with cytochrome bc₁ (complex III, CIII). Here, we present the cryogenic electron microscopy (cryo-EM) structure of S. cerevisiae CIV in a III₂IV₂ SC at 3.3 Å resolution. While overall similarity to mammalian homologs is high, we found notable differences in the supernumerary subunits Cox26 and Cox13; the latter exhibits a unique arrangement that precludes CIV dimerization as seen in bovine. A conformational shift in the matrix domain of Cox5A-involved in allosteric inhibition by ATP-may arise from its association with CIII. The CIII-CIV arrangement highlights a conserved interaction interface of CIII, albeit one occupied by complex I in mammalian respirasomes. We discuss our findings in the context of the potential impact of SC formation on CIV regulation.

Fig. 1. Overall structure of the S. cerevisiae III₂IV₂ supercomplex.

a, Side and top view of the III₂IV₂ supercomplex (SC) merged cryo-EM map with overall SC dimensions of 289x157x114 Å. CIII and CIV are represented in blue and orange, each monomer being represented by a different shade. The transparent grey density displays the extent of the GDN detergent belt. b, Side and top view of the III₂IV₂ SC model. CIII and CIV are represented in the same colours as in a, with Cox26 (green) and Qcr10 (red) highlighted.

Fig. 2. Structure of S. cerevisiae CIV.

a, Atomic model of CIV showing all 12 subunits. Cox1 is shown in yellow, Cox2 in cyan, Cox5A in pink, Cox26 in green, Cox9 in purple and Cox13 in orange. b, Interactions of Cox26 with Cox1, Cox2, Cox6, Cox9 (coloured as in a) and lipids (spacefill representation). c, Alignment of Cox5A (pink) with its bovine homologue (COX4-1 – grey and brown, PDB 1V54). The first ~50 amino acids are highlighted by a darker shade. d, Differences in length and shape of the transmembrane helix of Cox13 with its bovine homologue (COX6A, PDB 1V54).

Fig. 3. Interactions of Qcr10 with other subunits of CIII, and that of Rip1 with a lipid at the interface with CIV.

a, Position of Qcr10 (pink ribbon) in the CIII structure with its N- and C-termini highlighted. Other subunits of CIII that interact with Qcr10 are highlighted in colours. A molecule of ubiquinone at the Qi site is shown as blue spheres. The boxes indicate specific regions of interaction that are highlighted in the other panels. b, Qcr10 (pink) forms interactions with the transmembrane helix of Rip1 (yellow) and with Qcr9 (green) at both the matrix and IMS faces of the membrane. c, The N-terminal tail of Qcr10 interacts with Cor2 (purple) and Qcr7 (cyan) in the matrix. d, Interactions in the IMS between Qcr10 and Cytc₁ (grey), Rip1 (yellow) and Qcr9 (green). e, A slight shift in the N-terminus of Rip1 (yellow) compared to the yeast X-ray structure (blue) accommodates interactions with a cardiolipin that goes on to interact with Cox5A of CIV (light pink), forming part of the interface between the two complexes.

Fig. 4. Protein-protein interactions between CIV and CIII.

a and b, View from the matrix side of protein-protein interactions involving Cor1 (white) and Cox5A (pink). Residues that make inter-subunit interactions are indicated and their interactions are shown as dashed lines. c, Interactions between cytochrome c₁ (Cytc₁, brown) and Qcr6 (pale green) with Cox5A (pink) in the IMS. d, A cardiolipin molecule (CDL, yellow) and a phosphocholine (PCF, grey) within the membrane interacts with residues of Cox5A (pink), Rip1 (pale blue) and Qcr8 (blue).

Fig. 5. Alignment of the mammalian I₁III₂IV₁ respirasome with the III₂IV₂ SC from S. cerevisiae.

a, The structures of the tight ovine I₁III₂IV₁ respirasome (PDB 5J4Z, displayed in shades of grey) and the yeast III₂IV₂ SC (coloured as in Figure 1). b, These structures were aligned on their CIII dimers. The view in both a and b is from the IMS.