Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Structure of the membrane domain of respiratory complex I

Abstract

Complex I is the first and largest enzyme of the respiratory chain, coupling electron transfer between NADH and ubiquinone to the translocation of four protons across the membrane. It has a central role in cellular energy production and has been implicated in many human neurodegenerative diseases. The L-shaped enzyme consists of hydrophilic and membrane domains. Previously, we determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-like subunits L, M and N is novel, with two inverted structural repeats of five transmembrane helices arranged, unusually, face-to-back. Each repeat includes a discontinuous transmembrane helix and forms half of a channel across the membrane. A network of conserved polar residues connects the two half-channels, completing the proton translocation pathway. Unexpectedly, lysines rather than carboxylate residues act as the main elements of the proton pump in these subunits. The fourth probable proton-translocation channel is at the interface of subunits N, K, J and A. The structure indicates that proton translocation in complex I, uniquely, involves coordinated conformational changes in six symmetrical structural elements.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Architecture of the membrane domain of E. coli complex I.
Figure 2: Fold of antiporter-like subunits.
Figure 3: Connecting elements and interactions between subunits.
Figure 4: Proton translocation channels.
Figure 5: Proposed mechanism of complex I.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The coordinates and structure factors have been deposited in the RCSB Protein Data Bank under accession code 3RKO.

References

  1. 1

    Walker, J. E. The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. Q. Rev. Biophys. 25, 253–324 (1992)

    CAS  Article  Google Scholar 

  2. 2

    Yagi, T. & Matsuno-Yagi, A. The proton-translocating NADH–quinone oxidoreductase in the respiratory chain: the secret unlocked. Biochemistry 42, 2266–2274 (2003)

    CAS  Article  Google Scholar 

  3. 3

    Brandt, U. Energy converting NADH:quinone oxidoreductase (complex I). Annu. Rev. Biochem. 75, 69–92 (2006)

    CAS  Article  Google Scholar 

  4. 4

    Ohnishi, T. Iron-sulfur clusters/semiquinones in complex I. Biochim. Biophys. Acta 1364, 186–206 (1998)

    CAS  Article  Google Scholar 

  5. 5

    Sazanov, L. A. Respiratory complex I: mechanistic and structural insights provided by the crystal structure of the hydrophilic domain. Biochemistry 46, 2275–2288 (2007)

    CAS  Article  Google Scholar 

  6. 6

    Schapira, A. H. Human complex I defects in neurodegenerative diseases. Biochim. Biophys. Acta 1364, 261–270 (1998)

    CAS  Article  Google Scholar 

  7. 7

    Dawson, T. M. & Dawson, V. L. Molecular pathways of neurodegeneration in Parkinson’s disease. Science 302, 819–822 (2003)

    ADS  CAS  Article  Google Scholar 

  8. 8

    Balaban, R. S., Nemoto, S. & Finkel, T. Mitochondria, oxidants, and aging. Cell 120, 483–495 (2005)

    CAS  Article  Google Scholar 

  9. 9

    Carroll, J. et al. Bovine complex I is a complex of 45 different subunits. J. Biol. Chem. 281, 32724–32727 (2006)

    CAS  Article  Google Scholar 

  10. 10

    Yip, C. Y., Harbour, M. E., Jayawardena, K., Fearnley, I. M. & Sazanov, L. A. Evolution of respiratory complex I: “supernumerary” subunits are present in the alpha-proteobacterial enzyme. J. Biol. Chem. 286, 5023–5033 (2011)

    CAS  Article  Google Scholar 

  11. 11

    Efremov, R. G., Baradaran, R. & Sazanov, L. A. The architecture of respiratory complex I. Nature 465, 441–445 (2010)

    ADS  CAS  Article  Google Scholar 

  12. 12

    Sazanov, L. A. & Hinchliffe, P. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus . Science 311, 1430–1436 (2006)

    ADS  CAS  Article  Google Scholar 

  13. 13

    Berrisford, J. M. & Sazanov, L. A. Structural basis for the mechanism of respiratory complex I. J. Biol. Chem. 284, 29773–29783 (2009)

    CAS  Article  Google Scholar 

  14. 14

    Fearnley, I. M. & Walker, J. E. Conservation of sequences of subunits of mitochondrial complex I and their relationships with other proteins. Biochim. Biophys. Acta 1140, 105–134 (1992)

    CAS  Article  Google Scholar 

  15. 15

    Mathiesen, C. & Hagerhall, C. Transmembrane topology of the NuoL, M and N subunits of NADH:quinone oxidoreductase and their homologues among membrane-bound hydrogenases and bona fide antiporters. Biochim. Biophys. Acta 1556, 121–132 (2002)

    CAS  Article  Google Scholar 

  16. 16

    Friedrich, T. Complex I: a chimaera of a redox and conformation-driven proton pump? J. Bioenerg. Biomembr. 33, 169–177 (2001)

    CAS  Article  Google Scholar 

  17. 17

    Hunte, C., Zickermann, V. & Brandt, U. Functional modules and structural basis of conformational coupling in mitochondrial complex I. Science 329, 448–451 (2010)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Baranova, E. A., Holt, P. J. & Sazanov, L. A. Projection structure of the membrane domain of Escherichia coli respiratory complex I at 8 Å resolution. J. Mol. Biol. 366, 140–154 (2007)

    CAS  Article  Google Scholar 

  19. 19

    von Heijne, G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225, 487–494 (1992)

    CAS  Article  Google Scholar 

  20. 20

    Yau, W. M., Wimley, W. C., Gawrisch, K. & White, S. H. The preference of tryptophan for membrane interfaces. Biochemistry 37, 14713–14718 (1998)

    CAS  Article  Google Scholar 

  21. 21

    Vik, S. B. The transmembrane helices of the L, M, and N subunits of Complex I from E. coli can be assigned on the basis of conservation and hydrophobic moment analysis. FEBS Lett. 585, 1180–1184 (2011)

    CAS  Article  Google Scholar 

  22. 22

    Vinothkumar, K. R. & Henderson, R. Structures of membrane proteins. Q. Rev. Biophys. 43, 65–158 (2010)

    CAS  Article  Google Scholar 

  23. 23

    Screpanti, E. & Hunte, C. Discontinuous membrane helices in transport proteins and their correlation with function. J. Struct. Biol. 159, 261–267 (2007)

    CAS  Article  Google Scholar 

  24. 24

    Luecke, H., Schobert, B., Richter, H. T., Cartailler, J. P. & Lanyi, J. K. Structure of bacteriorhodopsin at 1.55 Å resolution. J. Mol. Biol. 291, 899–911 (1999)

    CAS  Article  Google Scholar 

  25. 25

    Cooley, R. B., Arp, D. J. & Karplus, P. A. Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality. J. Mol. Biol. 404, 232–246 (2010)

    CAS  Article  Google Scholar 

  26. 26

    Morino, M. et al. Single site mutations in the hetero-oligomeric Mrp antiporter from alkaliphilic Bacillus pseudofirmus OF4 that affect Na+/H+ antiport activity, sodium exclusion, individual Mrp protein levels, or Mrp complex formation. J. Biol. Chem. 285, 30942–30950 (2010)

    CAS  Article  Google Scholar 

  27. 27

    Nakamaru-Ogiso, E. et al. the membrane subunit NuoL (ND5) is involved in the indirect proton pumping mechanism of Escherichia coli complex I. J. Biol. Chem. 285, 39070–39078 (2010)

    CAS  Article  Google Scholar 

  28. 28

    Amarneh, B. & Vik, S. B. Mutagenesis of subunit N of the Escherichia coli complex I. Identification of the initiation codon and the sensitivity of mutants to decylubiquinone. Biochemistry 42, 4800–4808 (2003)

    CAS  Article  Google Scholar 

  29. 29

    Mathiesen, C. & Hagerhall, C. The ‘antiporter module’ of respiratory chain complex I includes the MrpC/NuoK subunit—a revision of the modular evolution scheme. FEBS Lett. 549, 7–13 (2003)

    CAS  Article  Google Scholar 

  30. 30

    Euro, L., Belevich, G., Verkhovsky, M. I., Wikstrom, M. & Verkhovskaya, M. Conserved lysine residues of the membrane subunit NuoM are involved in energy conversion by the proton-pumping NADH:ubiquinone oxidoreductase (complex I). Biochim. Biophys. Acta 1777, 1166–1172 (2008)

    CAS  Article  Google Scholar 

  31. 31

    Torres-Bacete, J., Nakamaru-Ogiso, E., Matsuno-Yagi, A. & Yagi, T. Characterization of the NuoM (ND4) subunit in Escherichia coli NDH-1: conserved charged residues essential for energy-coupled activities. J. Biol. Chem. 282, 36914–36922 (2007)

    CAS  Article  Google Scholar 

  32. 32

    Kao, M. C., Nakamaru-Ogiso, E., Matsuno-Yagi, A. & Yagi, T. Characterization of the membrane domain subunit NuoK (ND4L) of the NADH-quinone oxidoreductase from Escherichia coli . Biochemistry 44, 9545–9554 (2005)

    CAS  Article  Google Scholar 

  33. 33

    Kervinen, M., Patsi, J., Finel, M. & Hassinen, I. E. A pair of membrane-embedded acidic residues in the NuoK subunit of Escherichia coli NDH-1, a counterpart of the ND4L subunit of the mitochondrial complex I, are required for high ubiquinone reductase activity. Biochemistry 43, 773–781 (2004)

    CAS  Article  Google Scholar 

  34. 34

    Fisher, N. & Rich, P. R. A motif for quinone binding sites in respiratory and photosynthetic systems. J. Mol. Biol. 296, 1153–1162 (2000)

    CAS  Article  Google Scholar 

  35. 35

    Ohnishi, T., Nakamaru-Ogiso, E. & Ohnishi, S. T. A new hypothesis on the simultaneous direct and indirect proton pump mechanisms in NADH-quinone oxidoreductase (complex I). FEBS Lett. 584, 4131–4137 (2010)

    CAS  Article  Google Scholar 

  36. 36

    Nakamaru-Ogiso, E., Sakamoto, K., Matsuno-Yagi, A., Miyoshi, H. & Yagi, T. The ND5 subunit was labeled by a photoaffinity analogue of fenpyroximate in bovine mitochondrial complex I. Biochemistry 42, 746–754 (2003)

    CAS  Article  Google Scholar 

  37. 37

    Steimle, S. et al. The role of subunit NuoL for proton translocation by the respiratory complex I. Biochemistry 50, 3386–3393 (2011)

    CAS  Article  Google Scholar 

  38. 38

    Michel, J., Deleon-Rangel, J., Zhu, S., Van Ree, K. & Vik, S. B. mutagenesis of the L, M, and N subunits of complex I from Escherichia coli indicates a common role in function. PLoS ONE 6, e17420 (2011)

    ADS  CAS  Article  Google Scholar 

  39. 39

    Krishnamoorthy, G. & Hinkle, P. C. Studies on the electron transfer pathway, topography of iron-sulfur centers, and site of coupling in NADH-Q oxidoreductase. J. Biol. Chem. 263, 17566–17575 (1988)

    CAS  PubMed  Google Scholar 

  40. 40

    Kao, M. C. et al. Characterization of the membrane domain subunit NuoJ (ND6) of the NADH-quinone oxidoreductase from Escherichia coli by chromosomal DNA manipulation. Biochemistry 44, 3562–3571 (2005)

    CAS  Article  Google Scholar 

  41. 41

    Pätsi, J., Kervinen, M., Finel, M. & Hassinen, I. E. Leber hereditary optic neuropathy mutations in the ND6 subunit of mitochondrial complex I affect ubiquinone reduction kinetics in a bacterial model of the enzyme. Biochem. J. 409, 129–137 (2008)

    Article  Google Scholar 

  42. 42

    Galkin, A. S., Grivennikova, V. G. & Vinogradov, A. D. H+/2e stoichiometry in NADH-quinone reductase reactions catalyzed by bovine heart submitochondrial particles. FEBS Lett. 451, 157–161 (1999)

    CAS  Article  Google Scholar 

  43. 43

    Treberg, J. R. & Brand, M. D. A model of the proton translocation mechanism of complex I. J. Biol. Chem. 286, 17579–17584 (2011)

    CAS  Article  Google Scholar 

  44. 44

    Ohnishi, S. T., Salerno, J. C. & Ohnishi, T. Possible roles of two quinone molecules in direct and indirect proton pumps of bovine heart NADH-quinone oxidoreductase (complex I). Biochim. Biophys. Acta 1797, 1891–1893 (2010)

    CAS  Article  Google Scholar 

  45. 45

    Sazanov, L. A., Carroll, J., Holt, P., Toime, L. & Fearnley, I. M. A role for native lipids in the stabilization and two-dimensional crystallization of the Escherichia coli NADH-ubiquinone oxidoreductase (Complex I). J. Biol. Chem. 278, 19483–19491 (2003)

    CAS  Article  Google Scholar 

  46. 46

    Van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L. & Clardy, J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229, 105–124 (1993)

    CAS  Article  Google Scholar 

  47. 47

    Leif, H., Sled, V. D., Ohnishi, T., Weiss, H. & Friedrich, T. Isolation and characterization of the proton-translocating NADH: ubiquinone oxidoreductase from Escherichia coli . Eur. J. Biochem. 230, 538–548 (1995)

    CAS  Article  Google Scholar 

  48. 48

    Collaborative Computational Project 4.. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  49. 49

    Strong, M. et al. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis . Proc. Natl Acad. Sci. USA 103, 8060–8065 (2006)

    ADS  CAS  Article  Google Scholar 

  50. 50

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    CAS  Article  Google Scholar 

  51. 51

    de La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494 (1997)

    CAS  Article  Google Scholar 

  52. 52

    Brunger, A. T. Version 1.2 of the crystallography and NMR system. Nature Protocols 2, 2728–2733 (2007)

    CAS  Article  Google Scholar 

  53. 53

    Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)

    Article  Google Scholar 

  54. 54

    Jones, T. A. & Kjeldgaard, M. Electron-density map interpretation. Methods Enzymol. 277, 173–208 (1997)

    CAS  Article  Google Scholar 

  55. 55

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr.D 60, 2126–2132 (2004)

    Article  Google Scholar 

  56. 56

    Cowtan, K. The Buccaneer software for automated model building. 1. Tracing protein chains. Acta Crystallogr. D 62, 1002–1011 (2006)

    Article  Google Scholar 

  57. 57

    Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291 (1993)

    CAS  Article  Google Scholar 

  58. 58

    Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12–21 (2010)

    CAS  Article  Google Scholar 

  59. 59

    Thompson, J. D., Higgins, D. G. & Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680 (1994)

    CAS  Article  Google Scholar 

  60. 60

    Eswar, N. et al. Comparative protein structure modeling using Modeller. Curr. Protoc. Bioinformatics Ch. 5, Unit 5.6. (2006)

Download references

Acknowledgements

This work was funded by the Medical Research Council. We thank the ESRF and the SLS for provision of synchrotron radiation facilities. We are grateful to the staff of beamlines ID29 (ESRF) and X06SA (SLS) for assistance.

Author information

Affiliations

Authors

Contributions

R.G.E. performed research and analysed data; L.A.S. designed the project, analysed data and wrote the manuscript, with contributions from R.G.E.

Corresponding author

Correspondence to Leonid A. Sazanov.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion, Supplementary Tables 1-8, Supplementary Figures 1-8 with legends and additional references. (PDF 7855 kb)

Supplementary Movie 1

This movie illustrates the overall architecture of the membrane domain, showing arrangement of subunits, connecting elements, key helices and key charged residues. Towards the end, the arrangement of peripheral domain is illustrated using T. thermophilus structure (PDB 3I9V) shown in grey with Fe-S clusters as spheres. (MOV 22129 kb)

Supplementary Movie 2

This movie illustrates the fold of antiporter-like subunits (using subunit NuoM), showing the fold from N- to C-terminus, key helices, key charged residues and internal symmetry. Two repeating domains are shown in magenta and green. (MOV 25622 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Efremov, R., Sazanov, L. Structure of the membrane domain of respiratory complex I. Nature 476, 414–420 (2011). https://doi.org/10.1038/nature10330

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing