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Cryo-EM structure of the yeast respiratory supercomplex

Abstract

Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III2IV and III2IV2, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.

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Fig. 1: Cryo-EM structures of different classes of the yeast supercomplex.
Fig. 2: Atomic model of the yeast supercomplex (III2IV), location of cofactors, and the electron transfer pathway.
Fig. 3: Interactions between CIII and CIV in the yeast supercomplex.
Fig. 4: Comparison between yeast supercomplex and mammalian respirasome.

Data availability

The maps have been deposited at the Electron Microscopy Data Bank under accession codes EMD-0004 (S. cerevisiae respiratory supercomplex III2IV), EMD-0005 (S. cerevisiae supercomplex class 1, III2IV), and EMD-0006 (S. cerevisiae supercomplex class 2, III2IV2). Atomic coordinates have been deposited at the PDB with accession code 6GIQ.

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Acknowledgements

We would like to thank Gunnar von Heijne, José Miguel de la Rosa-Trevin, and Stefan Fleischmann from the cryo-EM facility at SciLifelab, Solna, Sweden, for support. We would like to thank Pia Ädelroth, Stockholm University, and the members of our group for stimulating discussions. This work was supported by grants from the Knut and Alice Wallenberg Foundation, the Carl Tryggers Foundation, and the Swedish Research Council.

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L.M.B. purified supercomplexes. S.R., J.B., and J.C. collected and processed the data, and built and refined the model. M.C. and J.C. supervized data collection. S.R., J.B., P.B., and M.O. analysed and interpreted the structure. M.O. supervized and coordinated the project. S.R., J.B., J.C., and M.O. wrote the manuscript. All authors commented on the final version of the manuscript.

Corresponding author

Correspondence to Martin Ott.

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The authors declare no competing interests.

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Integrated supplementary information

Supplementary Figure 1 Protein purification and workflow of cryo-EM image processing.

a, BN PAGE of total mitochondria (T) and elution (E) after purification. b, A representative cryo-EM micrograph from dataset 3. The scale bar is set to 390 Å. c, Representative 2D classes show multiple orientations and classes. The box size is 370 pixels with a pixel size of 1.06 Å. d, Workflow of cryo-EM image processing.

Supplementary Figure 2 Global and local resolution of the refined density maps of class 1, class 2 and III2IV modeling map.

a, Gold-standard Fourier shell correlation curves of the density maps after the final homologous refinements. The resolution of class 1, class 2 and the III2IV modeling map are 3.34 Å, 3.50 Å and 3.23 Å, respectively. b, The FSC curves calculated for class 1 and the modeling map to the final refined model. ce, Local resolution maps of class 1, class 2 and the III2IV modeling map viewed from two rotations along the membrane and from the matrix side.

Supplementary Figure 3 Superposition of subunits of the yeast supercomplex (III2IV) with the corresponding proteins from cow (Bos taurus) and pig (Sus scrofa).

a, Superposition of yeast Cor1 (PDB 3CX5) with Cor1 from the yeast supercomplex, III2IV, showing comparison between Cor1 subunit bound to Cox5a and the unoccupied side of CIII. b, Superposition of yeast Rip1 (PDB 3CX5) and the S. scrofa Rip1, in the loading state (PDB 5GUP) with Rip1 from the yeast supercomplex, (III2IV) show significant movement of the head domain and the hinge region residues: 90–93 compared to the yeast crystal structure but similar to the Rip1 in the loading state from the mammalian respirasomes. c, Superposition of the cytochrome c oxidase from the yeast supercomplex, III2IV, with bovine cytochrome c oxidase (PDB 1V54). d, Superposition of Cox4 (PDB 1V54) with Cox5a from the yeast supercomplex, III2IV.

Supplementary Figure 4 Structure of Qcr10 and identification of a novel subunit in the yeast supercomplex (III2IV).

a, Density and de novo model of the Qcr10 subunit of cytochrome bc1 complex demonstrating the quality of the map. b, Density and polyalanine model of an unidentified subunit in the cytochrome c oxidase in III2IV.

Supplementary Figure 5 Example densities of CIII subunits with phospholipids and CIV subunits of the yeast supercomplex (III2IV).

a, Example densities of phosholipids and the transmembrane helices from the modeling map of III2IV of the CIII region, demonstrating the quality of the map and the interaction of side chains with phospholipids. b, Example densities of the transmembrane helices from the modeling map of III2IV of the CIV region.

Supplementary Figure 6 Ubiquinones (UQ6) trapped in the catalytic Qi site of CIII.

a, Section of the CIII dimer from the supercomplex III2IV showing the rim of the quinone reduction (Qi site) cavity. The rim of the cavity is formed by four subunits of CIII, Qcr10, Qcr9, Rip1 and Cob. The UQ6 molecule in the catalytic site and the hemes (bH and bL) are highlighted in red and blue, respectively. b, Map density carved around the model of the two cytochrome b subunits of CIII, demonstrating the density of two ubiquinone molecules (UQ6), highlighted in blue. The UQ6 model is shown in yellow.

Supplementary Figure 7 Protein sequence alignment of Cox5a and Cox5b from S. cerevisiae.

The interface residues between the Cox5 isoforms and Cor1 are highlighted in orange, and residues involved in possible key interactions are colored red. The sequence identity is 64% and the sequence similarity is 74%. Alignment was carried out with EMBOSS Needle and processed in Jalview.

Supplementary Figure 8 Lipid bridges in the yeast supercomplex (III2IV).

a, Density of the modeling map showing the lipid densities bridging the gaps between the two complexes. b, Zoomed-in view showing the two lipid bridges and the subunits involved in the protein-lipid interactions in the yeast supercomplex.

Supplementary Figure 9 Protein sequence alignment of UQCRC1/Cor1 from different mammals and fungi.

Mammalian species aligned are Homo sapiens (human), Bos taurus (cow), and Mus musculus (mouse). Fungal species aligned are Yarrowia lipolytica, Candida albicans, Scheffersomyces stipitis, Spathaspora passalidarum, Saccharomyces cerevisiae (baker’s yeast), Kluyveromyces marxianus, and Zygosaccharomyces rouxii. Yeast indicated with an asterisk corresponds to species with CI and yeast indicated with double asterisks contains no CI. The interface loop of UQCRC1/Cor1 is highlighted in orange. Alignment was carried out with Clustal Omega and processed in Jalview.

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Rathore, S., Berndtsson, J., Marin-Buera, L. et al. Cryo-EM structure of the yeast respiratory supercomplex. Nat Struct Mol Biol 26, 50–57 (2019). https://doi.org/10.1038/s41594-018-0169-7

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