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.
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Modeling using prokaryotic complex I structures produced an orthologous mammalian core structure containing ND3 Cys39.
“We modeled the location of ND3 Cys39 using structures of prokaryotic complex I (refs. 32–34). This modeling led to an orthologous mammalian core structure containing ND3 Cys39 (Fig. 3f,g and Supplementary Figs. 14 and 15).”
From Cardioprotection by S-nitrosation of a cysteine switch on mitochondrial complex I (2013) · cites this paper as [33]
Cites
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · see citing works
<i>Coot</i> : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571 · see citing works
PROCHECK: a program to check the stereochemical quality of protein structures
Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) · Journal of Applied Crystallography · doi:10.1107/s0021889892009944 · Cited by 24,581 · see citing works
<i>Phaser</i> crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612 · see citing works
The CCP4 suite: programs for protein crystallography
Number Collaborative Computational Project (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994003112 · Cited by 17,299 · see citing works
<i>MolProbity</i> : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115 · see citing works
Comparative Protein Structure Modeling Using Modeller
Eswar, N., Webb, B., Martı́-Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Šali, A. (2006) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi0506s15 · Cited by 4,564 · see citing works
Mitochondria, Oxidants, and Aging
Balaban, R. S., Nemoto, S., & Finkel, T. (2005) · Cell · doi:10.1016/j.cell.2005.02.001 · Cited by 4,388 · see citing works
<i>PHENIX</i> : building new software for automated crystallographic structure determination
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361 · see citing works
Fortelle, E. D. L., & Bricogne, G. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)76073-7 · Cited by 1,893 · see citing works
The Buccaneer software for automated model building. 1. Tracing protein chains
Cowtan, K. D. (2006) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444906022116 · Cited by 1,834 · see citing works
Membrane protein structure prediction
von HEIJNE, G. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90934-c · Cited by 1,679 · see citing works
Molecular Pathways of Neurodegeneration in Parkinson's Disease
Dawson, T. M., & Dawson, V. L. (2003) · Science · doi:10.1126/science.1087753 · Cited by 1,659 · see citing works
Structure of bacteriorhodopsin at 1.55 Å resolution
Luecke, H., Schobert, B., Richter, H.-T., Cartailler, J., & Lanyi, J. Κ. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3027 · Cited by 1,452 · see citing works
Version 1.2 of the Crystallography and NMR system
Brünger, A. T. (2007) · Nature Protocols · doi:10.1038/nprot.2007.406 · Cited by 1,335 · see citing works
Atomic Structures of the Human Immunophilin FKBP-12 Complexes with FK506 and Rapamycin
Duyne, G. D. V., Standaert, R. F., Karplus, P. A., Schreiber, S. L., & Clardy, J. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1012 · Cited by 1,190 · see citing works
The Preference of Tryptophan for Membrane Interfaces
Yau, W., Wimley, W. C., Gawrisch, K., & White, S. H. (1998) · Biochemistry · doi:10.1021/bi980809c · Cited by 929 · see citing works
Energy Converting NADH: Quinone Oxidoreductase (Complex I)
Brandt, U. (2006) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.75.103004.142539 · Cited by 815 · see citing works
The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains
Walker, J. E. (1992) · Quarterly Reviews of Biophysics · doi:10.1017/s003358350000425x · Cited by 777 · see citing works
Structure of the Hydrophilic Domain of Respiratory Complex I from <i>Thermus thermophilus</i>
Sazanov, L. A., & Hinchliffe, P. (2006) · Science · doi:10.1126/science.1123809 · Cited by 763 · see citing works
Self-citationStrong, M., Sawaya, M. R., Wang, S., Phillips, M. L., Cascio, D., & Eisenberg, D. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0602606103 · Cited by 701 · see citing works
The architecture of respiratory complex I
Efremov, R. G., Baradaran, R., & Sazanov, L. A. (2010) · Nature · doi:10.1038/nature09066 · Cited by 616 · see citing works
Self-citation[10] Electron-density map interpretation
Jones, T. A., & Kjeldgaard, M. (1997) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(97)77012-5 · Cited by 507 · see citing works
Bovine Complex I Is a Complex of 45 Different Subunits
Carroll, J., Fearnley, I. M., Skehel, M. J., Shannon, R. J., Hirst, J., & Walker, J. E. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m607135200 · Cited by 486 · see citing works
Iron–sulfur clusters/semiquinones in Complex I
Ohnishi, T. (1998) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(98)00027-9 · Cited by 425 · see citing works
Functional Modules and Structural Basis of Conformational Coupling in Mitochondrial Complex I
Hunte, C., Zickermann, V., & Brandt, U. (2010) · Science · doi:10.1126/science.1191046 · Cited by 370 · see citing works
Fearnley, I. M., & Walker, J. E. (1992) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/0005-2728(92)90001-i · Cited by 308 · see citing works
Beckman, K. B., & Ames, B. N. (2000) · Elsevier eBooks · doi:10.1016/b978-044482650-3/50027-4 · Cited by 307 · see citing works
The Buccaneer software for automated model building
Cowtan, K. D. (2006) · White Rose Research Online (University of Leeds, The University of Sheffield, University of York) · Cited by 304 · see citing works
The Proton-Translocating NADH−Quinone Oxidoreductase in the Respiratory Chain: The Secret Unlocked
Yagi, T., & Matsuno‐Yagi, A. (2003) · Biochemistry · doi:10.1021/bi027158b · Cited by 296 · see citing works
Leif, H., Sled, V. D., Ohnishi, T., Weiss, H., & Friedrich, T. (1995) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1995.0538h.x · Cited by 293 · see citing works
Structural Basis for the Mechanism of Respiratory Complex I
Berrisford, J. M., & Sazanov, L. A. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.032144 · Cited by 247 · see citing works
Self-citationSazanov, L. A. (2007) · Biochemistry · doi:10.1021/bi602508x · Cited by 231 · see citing works
Self-citationLeif, H., Sled, V. D., Ohnishi, T., et al. (1995) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1995.tb20594.x · Cited by 225 · see citing works
Mathiesen, C., & Hägerhäll, C. (2002) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(02)00343-2 · Cited by 203 · see citing works
Structures of membrane proteins
Vinothkumar, K. R., & Henderson, R. A. (2010) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583510000041 · Cited by 198 · see citing works
Cooley, R. B., Arp, D. J., & Karplus, P. A. (2010) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.09.034 · Cited by 175 · see citing works
Galkin, A. S., Grivennikova, V. G., & Vinogradov, A. D. (1999) · FEBS Letters · doi:10.1016/s0014-5793(99)00575-x · Cited by 173 · see citing works
Human complex I defects in neurodegenerative diseases
Schapira, A. H. V. (1998) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(98)00032-2 · Cited by 166 · see citing works
Complex I: A Chimaera of a Redox and Conformation-Driven Proton Pump?
Friedrich, T. (2001) · Journal of Bioenergetics and Biomembranes · doi:10.1023/a:1010722717257 · Cited by 161 · see citing works
A motif for quinone binding sites in respiratory and photosynthetic systems 1 1Edited by R. Huber
Fisher, N. E., & Rich, P. R. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3509 · Cited by 161 · see citing works
Discontinuous membrane helices in transport proteins and their correlation with function
Screpanti, E., & Hunte, C. (2007) · Journal of Structural Biology · doi:10.1016/j.jsb.2007.01.011 · Cited by 139 · see citing works
Krishnamoorthy, G., & Hinkle, P. C. (1988) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)77873-9 · Cited by 130 · see citing works
Mathiesen, C., & Hägerhäll, C. (2003) · FEBS Letters · doi:10.1016/s0014-5793(03)00767-1 · Cited by 127 · see citing works
Evolution of Respiratory Complex I
Yip, C.-Y., Harbour, M. E., Jayawardena, K. G. I., Fearnley, I. M., & Sazanov, L. A. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.194993 · Cited by 124 · see citing works
Self-citationEuro, L., Belevich, G., Verkhovsky, M. I., Wikström, M. K. F., & Verkhovskaya, M. L. (2008) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2008.06.001 · Cited by 106 · see citing works
Nakamaru‐Ogiso, E., Kao, M., Chen, H., Sinha, S. C., Yagi, T., & Ohnishi, T. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.157826 · Cited by 93 · see citing works
Characterization of the NuoM (ND4) Subunit in Escherichia coli NDH-1
Torres‐Bacete, J., Nakamaru‐Ogiso, E., Matsuno‐Yagi, A., & Yagi, T. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m707855200 · Cited by 92 · see citing works
Nakamaru‐Ogiso, E., Sakamoto, K., Matsuno‐Yagi, A., et al. (2002) · Biochemistry · doi:10.1021/bi0269660 · Cited by 92 · see citing works
Amarneh, B., & Vik, S. B. (2003) · Biochemistry · doi:10.1021/bi0340346 · Cited by 84 · see citing works
Sazanov, L. A., Carroll, J., Holt, P., Toime, L. J., & Fearnley, I. M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m208959200 · Cited by 81 · see citing works
Self-citationBaranova, E. A., Holt, P. J., & Sazanov, L. A. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.11.026 · Cited by 81 · see citing works
Self-citationKao, M., Nakamaru‐Ogiso, E., Matsuno‐Yagi, A., et al. (2005) · Biochemistry · doi:10.1021/bi050708w · Cited by 64 · see citing works
Role of Subunit NuoL for Proton Translocation by Respiratory Complex I
Steimle, S., Bajzath, C., Dörner, K., Schulte, M. T., Bothe, V., & Friedrich, T. (2011) · Biochemistry · doi:10.1021/bi200264q · Cited by 63 · see citing works
Kao, M., Bernardo, S. D., Nakamaru‐Ogiso, E., et al. (2005) · Biochemistry · doi:10.1021/bi0476477 · Cited by 59 · see citing works
Kervinen, M., Pätsi, J., Finel, M., et al. (2003) · Biochemistry · doi:10.1021/bi0355903 · Cited by 55 · see citing works
Michel, J., DeLeon-Rangel, J., Zhu, S., Ree, K. V., & Vik, S. B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017420 · Cited by 49 · see citing works
A Model of the Proton Translocation Mechanism of Complex I
Treberg, J. R., & Brand, M. D. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.227751 · Cited by 46 · see citing works
Ohnishi, T., Nakamaru‐Ogiso, E., & Ohnishi, S. T. (2010) · FEBS Letters · doi:10.1016/j.febslet.2010.08.039 · Cited by 46 · see citing works
Morino, M., Natsui, S., Ono, T., et al. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.118661 · Cited by 44 · see citing works
Ohnishi, S. T., Salerno, J. C., & Ohnishi, T. (2010) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2010.06.010 · Cited by 40 · see citing works
Pätsi, J., Kervinen, M., Finel, M., & Hassinen, I. E. (2007) · Biochemical Journal · doi:10.1042/bj20070866 · Cited by 36 · see citing works
The role of subunit NuoL for proton translocation by the respiratory complex I
Steimle, S., Willistein, M., & Friedrich, T. (2012) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2012.06.174 · Cited by 7 · see citing works
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- Authors
- Efremov, R. G., & Sazanov, L. A.
- Affiliations
- Max Planck Institute of Molecular Physiology (DE)
- MRC Mitochondrial Biology Unit (GB)
- Corresponding author
- Sazanov, Leonid A.
- Venue
- Nature
- Published
- 2011-08
- Volume
- 476
- Issue
- 7361
- Pages
- 414-420
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1987127397
- Cited by
- 370
- References
- 64
- Citations by year
- 2026: 8 · 2025: 7 · 2024: 15 · 2023: 8 · 2022: 22 · 2021: 21 · 2020: 21 · 2019: 18 · 2018: 25 · 2017: 22 · 2016: 31 · 2015: 36 · 2014: 39 · 2013: 39 · 2012: 50
- FWCI
- 21.32
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DORA PSI (Paul Scherrer Institute) (submittedVersion)
- Max Planck Institute for Plasma Physics (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- European Synchrotron Radiation Facility
- Medical Research Council
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Mitochondrial Function and Pathology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › ATP Synthase and ATPases Research
- Keywords
- mitochondrial complex I, membrane domains, crystal structure, proton translocation, proton pump, lysine residues, transmembrane helices, Escherichia coli, neurodegenerative diseases
- MeSH terms
- Cell Membrane, Escherichia coli, Lysine, Models, Molecular, NAD, NADH Dehydrogenase, Protein Binding, Protons, Ubiquinone, Ion Transport, Protein Structure, Tertiary, Protein Folding, Antiporters, Crystallography, X-Ray, Protein Subunits, Escherichia coli Proteins, Electron Transport Complex I
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