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Crystal structure of the entire respiratory complex I.

Baradaran R, Berrisford JM, Minhas GS, Sazanov LA - Nature (2013)

Bottom Line: Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues.The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements.The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

ABSTRACT
Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

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Quinone reaction chamberSubunits are coloured as in Fig. 1. Iron-sulphur cluster N2 is shown as red-orange spheres. a-b) Experimental electron density (2mFo-DFc in blue, contoured at 1σ, and mFo-DFc in green, contoured at 3σ) and models obtained from crystals with bound Piericidin A (a) and Decyl-ubiquinone (b). Difference electron density was calculated before ligand modelling. Nqo4 residues interacting with the headgroup are indicated. Potential polar interactions are shown labelled with distances in Å. c) Surface (solvent-accessible) representation of the interface between two main domains. The empty crevice (C, circled, Supplementary Discussion) between Nqo10 and 7_TM1/Nqo8, as well as helices framing the entry point to the quinone site (Q) are indicated. d) Quinone reaction chamber, with its internal solvent-accessible surface coloured red for negative, white for neutral, and blue for positive surface charges. Charged residues lining the cavity are shown with carbon in magenta and hydrophobic residues in yellow. Residues are labelled with prefix indicating subunit (omitted for Nqo8). Ala63, the site of the primary LHON disease mutation45, is labelled in red. e) Theoretical model of bound ubiquinone-10. Carbon atoms in cyan indicates the 8th isoprenoid unit. The quinone chamber is shown with surface in brown and helices framing its entry point are indicated. Movable helix 6_H127, interacting with 8_AH1, is also labelled.
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Figure 4: Quinone reaction chamberSubunits are coloured as in Fig. 1. Iron-sulphur cluster N2 is shown as red-orange spheres. a-b) Experimental electron density (2mFo-DFc in blue, contoured at 1σ, and mFo-DFc in green, contoured at 3σ) and models obtained from crystals with bound Piericidin A (a) and Decyl-ubiquinone (b). Difference electron density was calculated before ligand modelling. Nqo4 residues interacting with the headgroup are indicated. Potential polar interactions are shown labelled with distances in Å. c) Surface (solvent-accessible) representation of the interface between two main domains. The empty crevice (C, circled, Supplementary Discussion) between Nqo10 and 7_TM1/Nqo8, as well as helices framing the entry point to the quinone site (Q) are indicated. d) Quinone reaction chamber, with its internal solvent-accessible surface coloured red for negative, white for neutral, and blue for positive surface charges. Charged residues lining the cavity are shown with carbon in magenta and hydrophobic residues in yellow. Residues are labelled with prefix indicating subunit (omitted for Nqo8). Ala63, the site of the primary LHON disease mutation45, is labelled in red. e) Theoretical model of bound ubiquinone-10. Carbon atoms in cyan indicates the 8th isoprenoid unit. The quinone chamber is shown with surface in brown and helices framing its entry point are indicated. Movable helix 6_H127, interacting with 8_AH1, is also labelled.

Mentions: To determine exactly where quinone binds, intact complex I was co-crystallised, or crystals soaked with quinone analogues: inhibitor Piericidin A and decyl-ubiquinone (DQ). Although in vivo T. thermophilus complex I uses menaquinone-8, it is also fully active with DQ21, and, in contrast to E. coli complex I36, the T. thermophilus enzyme does not contain any bound endogenous quinone after purification. X-ray data (Supplementary Table 1) clearly show (Fig. 4ab) that Piericidin A and DQ bind in a very similar manner, ~15 Å away from the membrane surface, at the deep end of long narrow cavity. In this position, the quinone headgroup is ~12 Å (centre-to-centre) from the Fe-S cluster N2, appropriate for efficient electron transfer37. One of the DQ ketone groups is, as predicted26,34, hydrogen-bonded to 4_Tyr87, while another interacts, unexpectedly, with 4_His38. Both residues are invariant and essential for activity34,38.


Crystal structure of the entire respiratory complex I.

Baradaran R, Berrisford JM, Minhas GS, Sazanov LA - Nature (2013)

Quinone reaction chamberSubunits are coloured as in Fig. 1. Iron-sulphur cluster N2 is shown as red-orange spheres. a-b) Experimental electron density (2mFo-DFc in blue, contoured at 1σ, and mFo-DFc in green, contoured at 3σ) and models obtained from crystals with bound Piericidin A (a) and Decyl-ubiquinone (b). Difference electron density was calculated before ligand modelling. Nqo4 residues interacting with the headgroup are indicated. Potential polar interactions are shown labelled with distances in Å. c) Surface (solvent-accessible) representation of the interface between two main domains. The empty crevice (C, circled, Supplementary Discussion) between Nqo10 and 7_TM1/Nqo8, as well as helices framing the entry point to the quinone site (Q) are indicated. d) Quinone reaction chamber, with its internal solvent-accessible surface coloured red for negative, white for neutral, and blue for positive surface charges. Charged residues lining the cavity are shown with carbon in magenta and hydrophobic residues in yellow. Residues are labelled with prefix indicating subunit (omitted for Nqo8). Ala63, the site of the primary LHON disease mutation45, is labelled in red. e) Theoretical model of bound ubiquinone-10. Carbon atoms in cyan indicates the 8th isoprenoid unit. The quinone chamber is shown with surface in brown and helices framing its entry point are indicated. Movable helix 6_H127, interacting with 8_AH1, is also labelled.
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Figure 4: Quinone reaction chamberSubunits are coloured as in Fig. 1. Iron-sulphur cluster N2 is shown as red-orange spheres. a-b) Experimental electron density (2mFo-DFc in blue, contoured at 1σ, and mFo-DFc in green, contoured at 3σ) and models obtained from crystals with bound Piericidin A (a) and Decyl-ubiquinone (b). Difference electron density was calculated before ligand modelling. Nqo4 residues interacting with the headgroup are indicated. Potential polar interactions are shown labelled with distances in Å. c) Surface (solvent-accessible) representation of the interface between two main domains. The empty crevice (C, circled, Supplementary Discussion) between Nqo10 and 7_TM1/Nqo8, as well as helices framing the entry point to the quinone site (Q) are indicated. d) Quinone reaction chamber, with its internal solvent-accessible surface coloured red for negative, white for neutral, and blue for positive surface charges. Charged residues lining the cavity are shown with carbon in magenta and hydrophobic residues in yellow. Residues are labelled with prefix indicating subunit (omitted for Nqo8). Ala63, the site of the primary LHON disease mutation45, is labelled in red. e) Theoretical model of bound ubiquinone-10. Carbon atoms in cyan indicates the 8th isoprenoid unit. The quinone chamber is shown with surface in brown and helices framing its entry point are indicated. Movable helix 6_H127, interacting with 8_AH1, is also labelled.
Mentions: To determine exactly where quinone binds, intact complex I was co-crystallised, or crystals soaked with quinone analogues: inhibitor Piericidin A and decyl-ubiquinone (DQ). Although in vivo T. thermophilus complex I uses menaquinone-8, it is also fully active with DQ21, and, in contrast to E. coli complex I36, the T. thermophilus enzyme does not contain any bound endogenous quinone after purification. X-ray data (Supplementary Table 1) clearly show (Fig. 4ab) that Piericidin A and DQ bind in a very similar manner, ~15 Å away from the membrane surface, at the deep end of long narrow cavity. In this position, the quinone headgroup is ~12 Å (centre-to-centre) from the Fe-S cluster N2, appropriate for efficient electron transfer37. One of the DQ ketone groups is, as predicted26,34, hydrogen-bonded to 4_Tyr87, while another interacts, unexpectedly, with 4_His38. Both residues are invariant and essential for activity34,38.

Bottom Line: Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues.The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements.The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

ABSTRACT
Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

Show MeSH
Related in: MedlinePlus