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The architecture of respiratory supercomplexes

Nature volume 537, pages 644–648 (2016)Cite this article

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Abstract

Mitochondrial electron transport chain complexes are organized into supercomplexes responsible for carrying out cellular respiration. Here we present three architectures of mammalian (ovine) supercomplexes determined by cryo-electron microscopy. We identify two distinct arrangements of supercomplex CICIII2CIV (the respirasome)—a major ‘tight’ form and a minor ‘loose’ form (resolved at the resolution of 5.8 Å and 6.7 Å, respectively), which may represent different stages in supercomplex assembly or disassembly. We have also determined an architecture of supercomplex CICIII2 at 7.8 Å resolution. All observed density can be attributed to the known 80 subunits of the individual complexes, including 132 transmembrane helices. The individual complexes form tight interactions that vary between the architectures, with complex IV subunit COX7a switching contact from complex III to complex I. The arrangement of active sites within the supercomplex may help control reactive oxygen species production. To our knowledge, these are the first complete architectures of the dominant, physiologically relevant state of the electron transport chain.

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Figure 1: Cryo-EM density maps of distinct supercomplex architectures.
Figure 2: Interaction sites between the electron transport chain complexes.
Figure 3: Possible stabilizing interactions involving COX7a or SCAF1.
Figure 4: Paths between substrate binding sites within the respirasome.
Figure 5: Schematic of electron flow through the asymmetric CIII in the tight respirasome.

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Accession codes

Primary accessions

Electron Microscopy Data Bank

Protein Data Bank

Data deposits

The EM maps have been deposited in the Electron Microscopy Data Bank under accession codes EMD-8130, EMD-8128 and EMD-8129. The models have been deposited in the Protein Data Bank (PDB) under accession codes 5J4Z, 5J7Y and 5J8K.

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Acknowledgements

We thank the MRC LMB Cambridge for the use of the Titan Krios microscope. Data processing was performed using the IST high-performance computer cluster. J.A.L. holds a long-term fellowship from FEBS. K.F. is partially funded by a MRC UK PhD fellowship.

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Authors and Affiliations

  1. Institute of Science and Technology Austria, Klosterneuburg, 3400, Austria

    James A. Letts, Karol Fiedorczuk & Leonid A. Sazanov

  2. MRC Mitochondrial Biology Unit, Cambridge, CB2 0XY, UK

    Karol Fiedorczuk

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Contributions

J.A.L. purified supercomplexes, prepared cryo-EM grids, processed and analysed data, built models and co-wrote the manuscript; K.F. prepared cryo-EM grids, collected cryo-EM data and aided with model building; L.A.S. designed and supervised the project, analysed data and co-wrote the manuscript.

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Correspondence to Leonid A. Sazanov.

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The authors declare no competing financial interests.

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Nature thanks A. Engel, D. Winge and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Extended data figures and tables

Extended Data Figure 1 Supercomplex preparation and image processing procedures.

a, BN–PAGE of fractions from a typical sucrose gradient of digitonin extracted supercomplexes. Partially purified CI and molecular weight standards (thyroglobulin, 669 kDa; ferritin, 440 kDa; catalase, 240 kDa) were also included in the gel. Fraction eight (marked with an asterisk) was taken and used for subsequent supercomplex grid preparation. See the Supplementary Information for full uncropped scans of the gels. b, Representative micrograph of the 1,608 micrographs collected with slightly higher than average particle count; additionally, each micrograph differed slightly in ice thickness and defocus. Scale bar, 100 nm. c, Representative 2D class averages obtained from reference-free classification. d, Classification and refinement procedures used in this study.

Extended Data Figure 2 Local resolution and overall resolutions of supercomplex maps.

a–c, Local resolution estimation by Resmap53 of the tight respirasome (a), the loose respirasome (b) and CICIII2 (c). The supercomplexes are shown from the CI side (left) and the CIII side (right), with the full map (detergent micelle visible), and with the detergent micelle cut out by carving the maps around the protein model (middle images). d, Gold-standard FSC curves for the overall maps. e, f, Per-frame B-factors (e) and Guinier plot intercepts (Cf) (f) used for particle polishing in RELION46 calculated using all good particles.

Extended Data Figure 3 Tight respirasome models and maps for each complex.

Two views of each respirasome complex model fit into the cryo-EM density, with CI in blue (top), CIII in green (middle) and CIV in pink (bottom). The detergent micelle density has been removed for clarity.

Extended Data Figure 4 Loose respirasome models and maps for each complex.

Two views of each respirasome complex model fit into the cryo-EM density, with CI in blue (top), CIII in green (middle) and CIV in pink (bottom). The detergent micelle density has been removed for clarity. The CIV map has been filtered at 8 Å.

Extended Data Figure 5 Supercomplex CICIII2 models and maps for each complex.

Two views of each CICIII2 complex model fit into the cryo-EM density, with CI in blue (top) and CIII in green (bottom). The detergent micelle density has been removed for clarity.

Extended Data Figure 6 Uncut cryo-EM density for the tight respirasome at different contour levels.

Density within 5 Å of the poly-alanine models was coloured with CI in blue, CIII in green and CIV in pink, excess density is coloured grey. a, Low-contour level showing protein and the detergent micelle which is disordered and so has much weaker, fragmented density with no features. b, Medium contour showing mainly protein density. Note that grey density around complexes III and IV is completely featureless, indicating that the known structures account for all observed protein density. c, High contour showing FeS clusters and haem co-factors. Density for N1a cluster in CI, the FeS clusters of UQCRFS1 in CIII and the binuclear copper centre in CIV are not visible due to disorder. N1b cluster is occluded by N4 at this angle. In the loose respirasome, maps peaks for haem a and a3 are not visible in CIV due to disorder.

Extended Data Figure 7 CI model and density.

a–d, Four views of CI showing the density (top) and model (bottom) from within the membrane plane along the side of the membrane arm (a, b), within the membrane plane from the interface of the hydrophilic and hydrophobic arm (c) and from the intermembrane space side (d). a–c, Images are shown with the matrix up and the intermembrane space down. Subunits and density are coloured as indicated. Subunits within the specified colours are: (1) core subunits 75 kDa, 49 kDa, 30 kDa, PSST, TYKY, 51 kDa, 24 kDa, ND1, ND2, ND3, ND4, ND4L, ND5, ND6; (2) supernumerary subunits 39 kDa, B8, B13, 42 kDa, B16.6, B14.7, SDAP-α/β; (3) core subunits 75 kDa and 30 kDa, extended C termini. Supernumerary subunits rebuilt or extended B14, 18 kDa, 13 kDa, B16.6, PGIV, 15 kDa, B14.5b, 42 kDa, ESSS, B22; (4) B17.2, PDSW, B18; (5 and 6) KFYI, B15; (7 and 8) MWFE, B9, B14.5a, MNLL, AGGG, B12, SGDH, B17, ASHI. These subunits have been assigned in our subsequent work32; (9) the unmodelled density, which represents ~7% of the total volume of the CI density. Unmodelled density is primarily located on the solvent-exposed surfaces and represents mainly N- and C termini of known subunits. Similar unmodelled density is also observed in the 5 Å cryo-EM structure of isolated bovine CI (ref. 23).

Extended Data Figure 8 Comparison to previous low-resolution respirasome structures.

a, Models for complexes determined in this study were fit into the cryo-EM density of ref. 18 (a, left) and ref. 19 (a, right), and are consistent with the depictions in those publications, as well as for structures deposited in the PDB. In the structure of the respirasome prepared in amphipols (a, left), all of the complexes are much more separate without forming any of the tight contacts seen here (Fig. 2). This difference may be attributed to the disruptive effects of amphipols or other differences in the preparation or processing. These best fits are compared to our models for the tight (b) and loose (c) respirasomes (both left and right for direct comparison to the models above). For the previous structures in a, 3D-classification was not performed. Therefore, to determine whether the low-resolution maps correspond to an average of the different states observed here, we also fitted our models into a map generated from auto-refinement of all our particles. d, Tight + loose + CICIII2 combined map (Extended Data Fig. 1). This map is dominated by the tight conformation and the model remains distinct from the fits into the previously published low-resolution maps18,19.

Extended Data Figure 9 Modelling of putative higher-order organization of respiratory chain.

One possibility for respiratory strings model could be based on the dimerization of CIV observed in crystal structures24. CIV from the tight respirasome (cyan) was aligned with one of the monomers of CIV from PDB accession code 2X2Q. The second monomer of the crystallographic CIV dimer was then aligned with another copy of respirasome (magenta). a, View from the mitochondrial matrix. b, Side view in the membrane plane. In such an arrangement, there are no clashes between the two copies of the respirasome, with complexes III and IV forming a flat interaction area. The excessive curvature of the model (contrasting with the aligned in plane transmembrane domains in individual respirasomes) may be explained if the contacts between monomers in the crystallographic CIV dimer deviate somewhat from the contacts in the putative CIV dimer within the membrane. Such a symmetric ‘twin’ respirasome may form a building block for putative respiratory strings.

Extended Data Figure 10 COX7a homologues.

a, Sequence alignment of ovine COX7a1, COX7a2 and SCAF1 (also known as COX7a-2RP, COX7a2l). Amino acid changes relative to the COX7a1 sequence are indicated with an asterisk. The N termini of mature COX7a1 and COX7a2 have been determined experimentally69, however, the exact N terminus of mature SCAF1 is unknown. Mass-spectrometry-identified peptides from BN–PAGE indicate that the N terminus contains at least an additional 11 amino acids14, however, these residues are predicted to be unstructured and hence have not been included in the sequence alignment. The sequence numbering is based on mature COX7a1 and full-length protein for SCAF1. b, c, Amino acid differences between COX7a1 and COX7a2 (b) or SCAF1 (c) are mapped onto the structure of bovine COX7a1 indicating that most differences point away from CIV and may contribute to its interactions with other electron transport chain complexes.

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This file contains the uncropped scans with size marker indications for Extended Data Figure 1a. (PDF 421 kb)

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Letts, J., Fiedorczuk, K. & Sazanov, L. The architecture of respiratory supercomplexes. Nature 537, 644–648 (2016). https://doi.org/10.1038/nature19774

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