Atomic structure of the entire mammalian mitochondrial complex I (original) (raw)

• Sazanov, L. A. A giant molecular proton pump: structure and mechanism of respiratory complex I. Nat. Rev. Mol. Cell Biol. 16, 375–388 (2015)
  Article CAS PubMed Google Scholar
• Moser, C. C., Farid, T. A., Chobot, S. E. & Dutton, P. L. Electron tunneling chains of mitochondria. Biochim. Biophys. Acta 1757, 1096–1109 (2006)
  Article CAS PubMed Google Scholar
• Letts, J. A. & Sazanov, L. A. Gaining mass: the structure of respiratory complex I-from bacterial towards mitochondrial versions. Curr. Opin. Struct. Biol. 33, 135–145 (2015)
  Article CAS PubMed Google Scholar
• Fassone, E. & Rahman, S. Complex I deficiency: clinical features, biochemistry and molecular genetics. J. Med. Genet. 49, 578–590 (2012)
  Article CAS PubMed Google Scholar
• Walker, J. E. The NADH:ubiquinone oxidoreductase (complex I) of respiratory chains. Q. Rev. Biophys. 25, 253–324 (1992)
  Article CAS PubMed Google Scholar
• Vinothkumar, K. R., Zhu, J. & Hirst, J. Architecture of mammalian respiratory complex I. Nature 515, 80–84 (2014)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Galkin, A., Dröse, S. & Brandt, U. The proton pumping stoichiometry of purified mitochondrial complex I reconstituted into proteoliposomes. Biochim. Biophys. Acta 1757, 1575–1581 (2006)
  Article CAS PubMed Google Scholar
• Wikström, M., Sharma, V., Kaila, V. R., Hosler, J. P. & Hummer, G. New perspectives on proton pumping in cellular respiration. Chem. Rev. 115, 2196–2221 (2015)
  Article PubMed Google Scholar
• Baradaran, R., Berrisford, J. M., Minhas, G. S. & Sazanov, L. A. Crystal structure of the entire respiratory complex I. Nature 494, 443–448 (2013)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Sazanov, L. A. & Hinchliffe, P. Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus. Science 311, 1430–1436 (2006)
  Article CAS ADS PubMed Google Scholar
• Efremov, R. G. & Sazanov, L. A. Structure of the membrane domain of respiratory complex I. Nature 476, 414–420 (2011)
  Article CAS ADS PubMed Google Scholar
• Zickermann, V. et al. Structural biology. Mechanistic insight from the crystal structure of mitochondrial complex I. Science 347, 44–49 (2015)
  Article CAS ADS PubMed Google Scholar
• Zhu, J. et al. Structure of subcomplex Iβ of mammalian respiratory complex I leads to new supernumerary subunit assignments. Proc. Natl Acad. Sci. USA 112, 12087–12092 (2015)
  Article CAS ADS PubMed PubMed Central Google Scholar
• DiMaio, F. et al. Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement. Nat. Methods 12, 361–365 (2015)
  Article CAS PubMed PubMed Central Google Scholar
• Zhu, J., Vinothkumar, K. R. & Hirst, J. Structure of mammalian respiratory complex I. Nature 536, 354–358 (2016)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Letts, J. A., Fiedorczuk, K. & Sazanov, L. A. Architecture of respiratory supercomplexes. Nature http://dx.doi.org/10.1038/nature19774 (2016)
• Carroll, J., Fearnley, I. M., Shannon, R. J., Hirst, J. & Walker, J. E. Analysis of the subunit composition of complex I from bovine heart mitochondria. Mol. Cell. Proteomics 2, 117–126 (2003)
• Chouchani, E. T. et al. Cardioprotection by _S_-nitrosation of a cysteine switch on mitochondrial complex I. Nat. Med. 19, 753–759 (2013)
  CAS Google Scholar
• Vinogradov, A. D. & Grivennikova, V. G. The mitochondrial complex I: progress in understanding of catalytic properties. IUBMB Life 52, 129–134 (2001)
  Article CAS PubMed Google Scholar
• Sánchez-Caballero, L., Guerrero-Castillo, S. & Nijtmans, L. Unraveling the complexity of mitochondrial complex I assembly: A dynamic process. Biochim. Biophys. Acta 1857, 980–990 (2016)
  Article PubMed Google Scholar
• Zickermann, V., Angerer, H., Ding, M. G., Nübel, E. & Brandt, U. Small single transmembrane domain (STMD) proteins organize the hydrophobic subunits of large membrane protein complexes. FEBS Lett. 584, 2516–2525 (2010)
  Article CAS PubMed Google Scholar
• Cronan, J. E. The chain-flipping mechanism of ACP (acyl carrier protein)-dependent enzymes appears universal. Biochem. J. 460, 157–163 (2014)
  Article CAS PubMed Google Scholar
• Angerer, H. Eukaryotic LYR proteins interact with mitochondrial protein complexes. Biology (Basel) 4, 133–150 (2015)
  CAS Google Scholar
• Oteiza, P. I. Zinc and the modulation of redox homeostasis. Free Radic. Biol. Med. 53, 1748–1759 (2012)
  Article CAS PubMed PubMed Central Google Scholar
• Kmita, K. et al. Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I. Proc. Natl Acad. Sci. USA 112, 5685–5690 (2015)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Sharpley, M. S., Shannon, R. J., Draghi, F. & Hirst, J. Interactions between phospholipids and NADH:ubiquinone oxidoreductase (complex I) from bovine mitochondria. Biochemistry 45, 241–248 (2006)
  Article CAS PubMed Google Scholar
• Brandt, U. Energy converting NADH:quinone oxidoreductase (complex I). Annu. Rev. Biochem. 75, 69–92 (2006)
  Article CAS PubMed Google Scholar
• Belevich, G., Knuuti, J., Verkhovsky, M. I., Wikström, M. & Verkhovskaya, M. Probing the mechanistic role of the long α-helix in subunit L of respiratory Complex I from Escherichia coli by site-directed mutagenesis. Mol. Microbiol. 82, 1086–1095 (2011)
  Article CAS PubMed PubMed Central Google Scholar
• Efremov, R. G., Baradaran, R. & Sazanov, L. A. The architecture of respiratory complex I. Nature 465, 441–445 (2010)
  Article CAS ADS PubMed Google Scholar
• Palmisano, G., Sardanelli, A. M., Signorile, A., Papa, S. & Larsen, M. R. The phosphorylation pattern of bovine heart complex I subunits. Proteomics 7, 1575–1583 (2007)
  Article CAS PubMed Google Scholar
• Berrisford, J. M. & Sazanov, L. A. Structural basis for the mechanism of respiratory complex I. J. Biol. Chem. 284, 29773–29783 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Sazanov, L. A., Peak-Chew, S. Y., Fearnley, I. M. & Walker, J. E. Resolution of the membrane domain of bovine complex I into subcomplexes: implications for the structural organization of the enzyme. Biochemistry 39, 7229–7235 (2000)
  Article CAS PubMed Google Scholar
• Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012)
  Article CAS PubMed PubMed Central Google Scholar
• Rohou, A. & Grigorieff, N. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015)
  Article PubMed PubMed Central Google Scholar
• Li, X. et al. Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM. Nat. Methods 10, 584–590 (2013)
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016)
  Article CAS ADS PubMed PubMed Central Google Scholar
• Rosenthal, P. B. & Henderson, R. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J. Mol. Biol. 333, 721–745 (2003)
  Article CAS PubMed Google Scholar
• Scheres, S. H. Beam-induced motion correction for sub-megadalton cryo-EM particles. eLife 3, e03665 (2014)
  PubMed PubMed Central Google Scholar
• Scheres, S. H. & Chen, S. Prevention of overfitting in cryo-EM structure determination. Nat. Methods 9, 853–854 (2012)
  Article CAS PubMed PubMed Central Google Scholar
• Bai, X. C., Rajendra, E., Yang, G., Shi, Y. & Scheres, S. H. Sampling the conformational space of the catalytic subunit of human γ-secretase. eLife 4, e11182 (2015)
  Article PubMed PubMed Central Google Scholar
• Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)
  Article CAS PubMed Google Scholar
• Allegretti, M., Mills, D. J., McMullan, G., Kühlbrandt, W. & Vonck, J. Atomic model of the F420-reducing [NiFe] hydrogenase by electron cryo-microscopy using a direct electron detector. eLife 3, e01963 (2014)
  Article PubMed PubMed Central Google Scholar
• Meents, A., Gutmann, S., Wagner, A. & Schulze-Briese, C. Origin and temperature dependence of radiation damage in biological samples at cryogenic temperatures. Proc. Natl Acad. Sci. USA 107, 1094–1099 (2010)
  Article CAS ADS PubMed Google Scholar
• Krivov, G. G., Shapovalov, M. V. & Dunbrack, R. L. Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77, 778–795 (2009)
  Article CAS PubMed PubMed Central Google Scholar
• Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protocols 10, 845–858 (2015)
  Article CAS PubMed Google Scholar
• Biasini, M. et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42, W252–W258 (2014)
  Article CAS PubMed PubMed Central Google Scholar
• Rost, B., Yachdav, G. & Liu, J. The PredictProtein server. Nucleic Acids Res. 32, W321–W326 (2004)/
  Article CAS PubMed PubMed Central Google Scholar
• McGuffin, L. J., Bryson, K. & Jones, D. T. The PSIPRED protein structure prediction server. Bioinformatics 16, 404–405 (2000)
  Article CAS PubMed Google Scholar
• Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580 (2001)
  Article CAS PubMed Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)
  Article PubMed Google Scholar
• Shinzawa-Itoh, K. et al. Bovine heart NADH-ubiquinone oxidoreductase contains one molecule of ubiquinone with ten isoprene units as one of the cofactors. Biochemistry 49, 487–492 (2010)
  Article CAS PubMed Google Scholar
• Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010)
  CAS PubMed PubMed Central Google Scholar
• Leitner, A., Walzthoeni, T. & Aebersold, R. Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat. Protocols 9, 120–137 (2014)
  Article CAS PubMed Google Scholar
• Kahraman, A., Malmström, L. & Aebersold, R. Xwalk: computing and visualizing distances in cross-linking experiments. Bioinformatics 27, 2163–2164 (2011)
  Article CAS PubMed PubMed Central Google Scholar