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Structure paper

TitleA universal coupling mechanism of respiratory complex I.
Journal, issue, pagesNature, Vol. 609, Issue 7928, Page 808-814, Year 2022
Publish dateSep 14, 2022
AuthorsVladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov /
PubMed AbstractComplex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone ...Complex I is the first enzyme in the respiratory chain, which is responsible for energy production in mitochondria and bacteria. Complex I couples the transfer of two electrons from NADH to quinone and the translocation of four protons across the membrane, but the coupling mechanism remains contentious. Here we present cryo-electron microscopy structures of Escherichia coli complex I (EcCI) in different redox states, including catalytic turnover. EcCI exists mostly in the open state, in which the quinone cavity is exposed to the cytosol, allowing access for water molecules, which enable quinone movements. Unlike the mammalian paralogues, EcCI can convert to the closed state only during turnover, showing that closed and open states are genuine turnover intermediates. The open-to-closed transition results in the tightly engulfed quinone cavity being connected to the central axis of the membrane arm, a source of substrate protons. Consistently, the proportion of the closed state increases with increasing pH. We propose a detailed but straightforward and robust mechanism comprising a 'domino effect' series of proton transfers and electrostatic interactions: the forward wave ('dominoes stacking') primes the pump, and the reverse wave ('dominoes falling') results in the ejection of all pumped protons from the distal subunit NuoL. This mechanism explains why protons exit exclusively from the NuoL subunit and is supported by our mutagenesis data. We contend that this is a universal coupling mechanism of complex I and related enzymes.
External linksNature / PubMed:36104567
MethodsEM (single particle)
Resolution2.15 - 4.0 Å
Structure data

EMDB-13214, PDB-7p61:
Complex I from E. coli, DDM-purified, with NADH, Resting state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-13215, PDB-7p62:
Complex I from E. coli, DDM-purified, Apo, Resting state
Method: EM (single particle) / Resolution: 3.6 Å

EMDB-13216, PDB-7p63:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Closed state
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-13217, PDB-7p64:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Open state
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-13222, PDB-7p69:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Resting state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-13235, PDB-7p7c:
Complex I from E. coli, DDM/LMNG-purified, Apo, Open state
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-13236, PDB-7p7e:
Complex I from E. coli, DDM/LMNG-purified, Apo, Resting state
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-13237, PDB-7p7j:
Complex I from E. coli, DDM/LMNG-purified, with DQ, Open state
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-13238, PDB-7p7k:
Complex I from E. coli, DDM/LMNG-purified, with DQ, Resting state
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-13239, PDB-7p7l:
Complex I from E. coli, DDM/LMNG-purified, with NADH and FMN, Open state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-13240, PDB-7p7m:
Complex I from E. coli, DDM/LMNG-purified, inhibited by Piericidin A, Open state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-14535, PDB-7z7r:
Complex I from E. coli, LMNG-purified, Apo, Open-ready state
Method: EM (single particle) / Resolution: 3.36 Å

EMDB-14536, PDB-7z7s:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-14537, PDB-7z7t:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-14538, PDB-7z7v:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state
Method: EM (single particle) / Resolution: 2.29 Å

EMDB-14540, PDB-7z80:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-14541, PDB-7z83:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-14542, PDB-7z84:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state
Method: EM (single particle) / Resolution: 2.87 Å

EMDB-14620, PDB-7zc5:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-14632, PDB-7zci:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-14637, PDB-7zd6:
Complex I from Ovis aries, at pH7.4, Open state
Method: EM (single particle) / Resolution: 3.16 Å

EMDB-14648, PDB-7zdh:
Complex I from Ovis aries at pH7.4, Closed state
Method: EM (single particle) / Resolution: 3.46 Å

EMDB-14651, PDB-7zdj:
Complex I from Ovis aries at pH5.5, Open state
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-14658, PDB-7zdm:
Complex I from Ovis aries at pH5.5, Closed state
Method: EM (single particle) / Resolution: 3.44 Å

EMDB-14664, PDB-7zdp:
Complex I from Ovis aries at pH9, Open state
Method: EM (single particle) / Resolution: 3.88 Å

EMDB-14688, PDB-7zeb:
Complex I from Ovis aries at pH9, Closed state
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-14815: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state, Entire consensus map
Method: EM (single particle) / Resolution: 2.29 Å

EMDB-14816: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state, PA focused map
Method: EM (single particle) / Resolution: 2.15 Å

EMDB-14817: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state, MD focused map
Method: EM (single particle) / Resolution: 2.38 Å

EMDB-14818: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state, PA focused map
Method: EM (single particle) / Resolution: 2.39 Å

EMDB-14819: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state, MD focused map
Method: EM (single particle) / Resolution: 2.95 Å

EMDB-14820: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state, Entire consensus map
Method: EM (single particle) / Resolution: 2.61 Å

EMDB-14821: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state, Entire consensus map
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-14822: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state, PA focused map
Method: EM (single particle) / Resolution: 2.71 Å

EMDB-14823: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state, MD focused map
Method: EM (single particle) / Resolution: 2.93 Å

EMDB-14824: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state, Entire consensus map
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-14825: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state, MD focused map
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-14826: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state, PA focused map
Method: EM (single particle) / Resolution: 2.65 Å

EMDB-14827: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state, Entire consensus map
Method: EM (single particle) / Resolution: 2.87 Å

EMDB-14828: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state, PA focused map
Method: EM (single particle) / Resolution: 2.69 Å

EMDB-14829: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state, MD focused map
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-14830: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state, PA focused map
Method: EM (single particle) / Resolution: 2.61 Å

EMDB-14831: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state, MD focused map
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-14832: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state, Entire consensus map
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-14833: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state, PA focused map
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-14834: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state, MD focused map
Method: EM (single particle) / Resolution: 3.14 Å

EMDB-14835: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state, Entire consensus map
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-14836: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state, PA focused map
Method: EM (single particle) / Resolution: 2.29 Å

EMDB-14837: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state, MD focused map
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-14838: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, Entire consensus map
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-14839: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, NuoFEG focused map
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-14840: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, Interface focused map
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-14841: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, Antiporters focused map
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-15064: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state, Entire consensus map
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-15068: Peripheral arm of Complex I from Ovis aries at pH7.4, Open state
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-15069: Membrane domain of Complex I from Ovis aries at pH7.4, Open state
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-15071: Consensus map of Complex I from Ovis aries at pH7.4, Open state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-15074: Membrane domain of Complex I from Ovis aries at pH7.4, Closed state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-15075: Consensus map of Complex I from Ovis aries at pH7.4, Closed state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-15077: Peripheral arm of Complex I from Ovis aries at pH7.4, Closed state
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-15078: Peripheral arm of Complex I from Ovis aries at pH5.5, Open state
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-15079: Membrane domain of Complex I from Ovis aries at pH5.5, Open state
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-15080: Consensus map of Complex I from Ovis aries at pH5.5, Open state
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-15081: Membrane domain of Complex I from Ovis aries at pH5.5, Closed state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-15082: Consensus map of Complex I from Ovis aries at pH5.5, Closed state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-15083: Peripheral arm of Complex I from Ovis aries at pH5.5, Closed state
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-15094: Peripheral arm of Complex I from Ovis aries at pH9, Open state
Method: EM (single particle) / Resolution: 3.75 Å

EMDB-15095: Membrane domain of Complex I from Ovis aries at pH9, Open state
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-15096: Consensus map of Complex I from Ovis aries at pH9, Open state
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-15097: Peripheral arm of Complex I from Ovis aries at pH9, Closed state
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-15098: Membrane domain of Complex I from Ovis aries at pH9, Closed state
Method: EM (single particle) / Resolution: 3.94 Å

EMDB-15099: Consensus map of Complex I from Ovis aries at pH9, Closed state
Method: EM (single particle) / Resolution: 3.9 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-CA:
Unknown entry

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

ChemComp-UQ8:
Ubiquinone-8

ChemComp-DCQ:
2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione

ChemComp-LFA:
EICOSANE

ChemComp-HOH:
WATER

ChemComp-HQH:
Piericidin A / antibiotic*YM

ChemComp-C14:
TETRADECANE

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

ChemComp-ZMP:
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-MYR:
MYRISTIC ACID

ChemComp-K:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Source
  • escherichia coli (E. coli)
  • escherichia coli bl21(de3) (bacteria)
  • escherichia coli str. k-12 substr. mc4100 (bacteria)
  • escherichia coliescherichia coli str. k-12 substr. mc4100 (bacteria)
  • escherichia coli bl21 (bacteria)
  • ovis aries (sheep)
  • sheep (sheep)
KeywordsPROTON TRANSPORT / Complex I / NADH / Quinone / MEMBRANE PROTEIN / respiration / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase

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