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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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a) Structure of the entire complex I from T. thermophilus. FMN and Fe-S clusters are shown as magenta and red-orange spheres, respectively, with cluster N2 labelled. Key helices around the entry point (Q) into the quinone reaction chamber, and approximate membrane position are indicated. b) Putative proton translocation channels in the antiporter-like subunits. Polar residues lining the channels are shown as sticks with carbon in dark blue for the first (N-terminal) half-channel, in green for the second (C-terminal) half-channel and in orange for connecting residues. Key residues, GluTM5 and LysTM7 from the first half-channel, Lys/HisTM8 from the connection and Lys/GluTM12 from the second half-channel, are labelled. Approximate proton translocation paths are indicated by blue arrows.
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Figure 1: a) Structure of the entire complex I from T. thermophilus. FMN and Fe-S clusters are shown as magenta and red-orange spheres, respectively, with cluster N2 labelled. Key helices around the entry point (Q) into the quinone reaction chamber, and approximate membrane position are indicated. b) Putative proton translocation channels in the antiporter-like subunits. Polar residues lining the channels are shown as sticks with carbon in dark blue for the first (N-terminal) half-channel, in green for the second (C-terminal) half-channel and in orange for connecting residues. Key residues, GluTM5 and LysTM7 from the first half-channel, Lys/HisTM8 from the connection and Lys/GluTM12 from the second half-channel, are labelled. Approximate proton translocation paths are indicated by blue arrows.

Mentions: The diffraction of crystals of the entire T. thermophilus complex has been improved to 3.3 Å resolution (Methods). Crystals are, however, twinned and so to overcome the problem of model bias, we crystallised the isolated T. thermophilus membrane domain. These crystals were non-twinned and contained subunit Nqo8. The structure was solved at 3.3 Å resolution by molecular replacement with our E. coli model (PDB 3RKO) (Supplementary Tables 1 and 2, Supplementary Fig. 2). It contains seven subunits (Nqo12 with 16 TM helices, Nqo13 - 14, Nqo14 – 14, Nqo10 – 5, Nqo11 – 3, Nqo7 – 3 and Nqo8 – 9). Antiporters Nqo12-14 show an arrangement of helices (Supplementary Fig. 3) and key residues similar to the E. coli structure - each subunit contains two inverted symmetry-related half-channels. The cytoplasm-linked TM4-8 half-channel contains a central lysine on the discontinuous, thus flexible, TM7 and its pKa-modulating glutamate on TM5, while the periplasm-linked TM9-13 half-channel contains a central lysine (Glu in Nqo13) on discontinuous TM12 (Fig. 1b). The half-channels are linked into a single full proton translocation channel by charged residues, including a lysine from the broken (partly unwound in the middle) TM8 (His in Nqo12). The long connecting helix HL, from the C-terminal extension of Nqo12, is straighter in T. thermophilus than in E. coli (Supplementary Fig. 3). On the opposite side of the domain, the β-hairpin-helix connecting element (βH) shows a very similar arrangement in both species. Thus, both previously proposed coupling elements29 appear to be a common complex I feature.


Crystal structure of the entire respiratory complex I.

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

a) Structure of the entire complex I from T. thermophilus. FMN and Fe-S clusters are shown as magenta and red-orange spheres, respectively, with cluster N2 labelled. Key helices around the entry point (Q) into the quinone reaction chamber, and approximate membrane position are indicated. b) Putative proton translocation channels in the antiporter-like subunits. Polar residues lining the channels are shown as sticks with carbon in dark blue for the first (N-terminal) half-channel, in green for the second (C-terminal) half-channel and in orange for connecting residues. Key residues, GluTM5 and LysTM7 from the first half-channel, Lys/HisTM8 from the connection and Lys/GluTM12 from the second half-channel, are labelled. Approximate proton translocation paths are indicated by blue arrows.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3672946&req=5

Figure 1: a) Structure of the entire complex I from T. thermophilus. FMN and Fe-S clusters are shown as magenta and red-orange spheres, respectively, with cluster N2 labelled. Key helices around the entry point (Q) into the quinone reaction chamber, and approximate membrane position are indicated. b) Putative proton translocation channels in the antiporter-like subunits. Polar residues lining the channels are shown as sticks with carbon in dark blue for the first (N-terminal) half-channel, in green for the second (C-terminal) half-channel and in orange for connecting residues. Key residues, GluTM5 and LysTM7 from the first half-channel, Lys/HisTM8 from the connection and Lys/GluTM12 from the second half-channel, are labelled. Approximate proton translocation paths are indicated by blue arrows.
Mentions: The diffraction of crystals of the entire T. thermophilus complex has been improved to 3.3 Å resolution (Methods). Crystals are, however, twinned and so to overcome the problem of model bias, we crystallised the isolated T. thermophilus membrane domain. These crystals were non-twinned and contained subunit Nqo8. The structure was solved at 3.3 Å resolution by molecular replacement with our E. coli model (PDB 3RKO) (Supplementary Tables 1 and 2, Supplementary Fig. 2). It contains seven subunits (Nqo12 with 16 TM helices, Nqo13 - 14, Nqo14 – 14, Nqo10 – 5, Nqo11 – 3, Nqo7 – 3 and Nqo8 – 9). Antiporters Nqo12-14 show an arrangement of helices (Supplementary Fig. 3) and key residues similar to the E. coli structure - each subunit contains two inverted symmetry-related half-channels. The cytoplasm-linked TM4-8 half-channel contains a central lysine on the discontinuous, thus flexible, TM7 and its pKa-modulating glutamate on TM5, while the periplasm-linked TM9-13 half-channel contains a central lysine (Glu in Nqo13) on discontinuous TM12 (Fig. 1b). The half-channels are linked into a single full proton translocation channel by charged residues, including a lysine from the broken (partly unwound in the middle) TM8 (His in Nqo12). The long connecting helix HL, from the C-terminal extension of Nqo12, is straighter in T. thermophilus than in E. coli (Supplementary Fig. 3). On the opposite side of the domain, the β-hairpin-helix connecting element (βH) shows a very similar arrangement in both species. Thus, both previously proposed coupling elements29 appear to be a common complex I feature.

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