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Structure paper

タイトルA universal coupling mechanism of respiratory complex I.
ジャーナル・号・ページNature, Vol. 609, Issue 7928, Page 808-814, Year 2022
掲載日2022年9月14日
著者Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov /
PubMed 要旨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 ...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.
リンクNature / PubMed:36104567
手法EM (単粒子)
解像度2.15 - 4.0 Å
構造データ

EMDB-13214, PDB-7p61:
Complex I from E. coli, DDM-purified, with NADH, Resting state
手法: EM (単粒子) / 解像度: 3.2 Å

EMDB-13215, PDB-7p62:
Complex I from E. coli, DDM-purified, Apo, Resting state
手法: EM (単粒子) / 解像度: 3.6 Å

EMDB-13216, PDB-7p63:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Closed state
手法: EM (単粒子) / 解像度: 3.4 Å

EMDB-13217, PDB-7p64:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Open state
手法: EM (単粒子) / 解像度: 2.5 Å

EMDB-13222, PDB-7p69:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 6, Resting state
手法: EM (単粒子) / 解像度: 3.0 Å

EMDB-13235, PDB-7p7c:
Complex I from E. coli, DDM/LMNG-purified, Apo, Open state
手法: EM (単粒子) / 解像度: 2.4 Å

EMDB-13236, PDB-7p7e:
Complex I from E. coli, DDM/LMNG-purified, Apo, Resting state
手法: EM (単粒子) / 解像度: 2.7 Å

EMDB-13237, PDB-7p7j:
Complex I from E. coli, DDM/LMNG-purified, with DQ, Open state
手法: EM (単粒子) / 解像度: 2.7 Å

EMDB-13238, PDB-7p7k:
Complex I from E. coli, DDM/LMNG-purified, with DQ, Resting state
手法: EM (単粒子) / 解像度: 3.1 Å

EMDB-13239, PDB-7p7l:
Complex I from E. coli, DDM/LMNG-purified, with NADH and FMN, Open state
手法: EM (単粒子) / 解像度: 3.0 Å

EMDB-13240, PDB-7p7m:
Complex I from E. coli, DDM/LMNG-purified, inhibited by Piericidin A, Open state
手法: EM (単粒子) / 解像度: 3.2 Å

EMDB-14535, PDB-7z7r:
Complex I from E. coli, LMNG-purified, Apo, Open-ready state
手法: EM (単粒子) / 解像度: 3.36 Å

EMDB-14536, PDB-7z7s:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state
手法: EM (単粒子) / 解像度: 2.4 Å

EMDB-14537, PDB-7z7t:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state
手法: EM (単粒子) / 解像度: 3.1 Å

EMDB-14538, PDB-7z7v:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state
手法: EM (単粒子) / 解像度: 2.29 Å

EMDB-14540, PDB-7z80:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state
手法: EM (単粒子) / 解像度: 2.93 Å

EMDB-14541, PDB-7z83:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state
手法: EM (単粒子) / 解像度: 2.88 Å

EMDB-14542, PDB-7z84:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state
手法: EM (単粒子) / 解像度: 2.87 Å

EMDB-14620, PDB-7zc5:
Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state
手法: EM (単粒子) / 解像度: 3.0 Å

EMDB-14632, PDB-7zci:
Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state
手法: EM (単粒子) / 解像度: 2.69 Å

EMDB-14637, PDB-7zd6:
Complex I from Ovis aries, at pH7.4, Open state
手法: EM (単粒子) / 解像度: 3.16 Å

EMDB-14648, PDB-7zdh:
Complex I from Ovis aries at pH7.4, Closed state
手法: EM (単粒子) / 解像度: 3.46 Å

EMDB-14651, PDB-7zdj:
Complex I from Ovis aries at pH5.5, Open state
手法: EM (単粒子) / 解像度: 3.25 Å

EMDB-14658, PDB-7zdm:
Complex I from Ovis aries at pH5.5, Closed state
手法: EM (単粒子) / 解像度: 3.44 Å

EMDB-14664, PDB-7zdp:
Complex I from Ovis aries at pH9, Open state
手法: EM (単粒子) / 解像度: 3.88 Å

EMDB-14688, PDB-7zeb:
Complex I from Ovis aries at pH9, Closed state
手法: EM (単粒子) / 解像度: 3.8 Å

EMDB-14815: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state, Entire consensus map
手法: EM (単粒子) / 解像度: 2.29 Å

EMDB-14816: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state, PA focused map
手法: EM (単粒子) / 解像度: 2.15 Å

EMDB-14817: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open-ready state, MD focused map
手法: EM (単粒子) / 解像度: 2.38 Å

EMDB-14818: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state, PA focused map
手法: EM (単粒子) / 解像度: 2.39 Å

EMDB-14819: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state, MD focused map
手法: EM (単粒子) / 解像度: 2.95 Å

EMDB-14820: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Resting state, Entire consensus map
手法: EM (単粒子) / 解像度: 2.61 Å

EMDB-14821: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state, Entire consensus map
手法: EM (単粒子) / 解像度: 2.93 Å

EMDB-14822: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state, PA focused map
手法: EM (単粒子) / 解像度: 2.71 Å

EMDB-14823: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Closed state, MD focused map
手法: EM (単粒子) / 解像度: 2.93 Å

EMDB-14824: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state, Entire consensus map
手法: EM (単粒子) / 解像度: 2.88 Å

EMDB-14825: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state, MD focused map
手法: EM (単粒子) / 解像度: 3.05 Å

EMDB-14826: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open state, PA focused map
手法: EM (単粒子) / 解像度: 2.65 Å

EMDB-14827: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state, Entire consensus map
手法: EM (単粒子) / 解像度: 2.87 Å

EMDB-14828: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state, PA focused map
手法: EM (単粒子) / 解像度: 2.69 Å

EMDB-14829: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Open-ready state, MD focused map
手法: EM (単粒子) / 解像度: 3.05 Å

EMDB-14830: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state, PA focused map
手法: EM (単粒子) / 解像度: 2.61 Å

EMDB-14831: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state, MD focused map
手法: EM (単粒子) / 解像度: 3.07 Å

EMDB-14832: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state, Entire consensus map
手法: EM (単粒子) / 解像度: 3.1 Å

EMDB-14833: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state, PA focused map
手法: EM (単粒子) / 解像度: 2.88 Å

EMDB-14834: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Open state, MD focused map
手法: EM (単粒子) / 解像度: 3.14 Å

EMDB-14835: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state, Entire consensus map
手法: EM (単粒子) / 解像度: 2.4 Å

EMDB-14836: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state, PA focused map
手法: EM (単粒子) / 解像度: 2.29 Å

EMDB-14837: Complex I from E. coli, LMNG-purified, under Turnover at pH 6, Closed state, MD focused map
手法: EM (単粒子) / 解像度: 2.5 Å

EMDB-14838: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, Entire consensus map
手法: EM (単粒子) / 解像度: 3.4 Å

EMDB-14839: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, NuoFEG focused map
手法: EM (単粒子) / 解像度: 3.4 Å

EMDB-14840: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, Interface focused map
手法: EM (単粒子) / 解像度: 3.4 Å

EMDB-14841: Complex I from E. coli, LMNG-purified, Apo, Open-ready state, Antiporters focused map
手法: EM (単粒子) / 解像度: 3.5 Å

EMDB-15064: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state, Entire consensus map
手法: EM (単粒子) / 解像度: 3.0 Å

EMDB-15068: Peripheral arm of Complex I from Ovis aries at pH7.4, Open state
手法: EM (単粒子) / 解像度: 3.1 Å

EMDB-15069: Membrane domain of Complex I from Ovis aries at pH7.4, Open state
手法: EM (単粒子) / 解像度: 3.3 Å

EMDB-15071: Consensus map of Complex I from Ovis aries at pH7.4, Open state
手法: EM (単粒子) / 解像度: 3.2 Å

EMDB-15074: Membrane domain of Complex I from Ovis aries at pH7.4, Closed state
手法: EM (単粒子) / 解像度: 3.5 Å

EMDB-15075: Consensus map of Complex I from Ovis aries at pH7.4, Closed state
手法: EM (単粒子) / 解像度: 3.5 Å

EMDB-15077: Peripheral arm of Complex I from Ovis aries at pH7.4, Closed state
手法: EM (単粒子) / 解像度: 3.4 Å

EMDB-15078: Peripheral arm of Complex I from Ovis aries at pH5.5, Open state
手法: EM (単粒子) / 解像度: 3.2 Å

EMDB-15079: Membrane domain of Complex I from Ovis aries at pH5.5, Open state
手法: EM (単粒子) / 解像度: 3.3 Å

EMDB-15080: Consensus map of Complex I from Ovis aries at pH5.5, Open state
手法: EM (単粒子) / 解像度: 3.3 Å

EMDB-15081: Membrane domain of Complex I from Ovis aries at pH5.5, Closed state
手法: EM (単粒子) / 解像度: 3.5 Å

EMDB-15082: Consensus map of Complex I from Ovis aries at pH5.5, Closed state
手法: EM (単粒子) / 解像度: 3.5 Å

EMDB-15083: Peripheral arm of Complex I from Ovis aries at pH5.5, Closed state
手法: EM (単粒子) / 解像度: 3.4 Å

EMDB-15094: Peripheral arm of Complex I from Ovis aries at pH9, Open state
手法: EM (単粒子) / 解像度: 3.75 Å

EMDB-15095: Membrane domain of Complex I from Ovis aries at pH9, Open state
手法: EM (単粒子) / 解像度: 4.0 Å

EMDB-15096: Consensus map of Complex I from Ovis aries at pH9, Open state
手法: EM (単粒子) / 解像度: 4.0 Å

EMDB-15097: Peripheral arm of Complex I from Ovis aries at pH9, Closed state
手法: EM (単粒子) / 解像度: 3.66 Å

EMDB-15098: Membrane domain of Complex I from Ovis aries at pH9, Closed state
手法: EM (単粒子) / 解像度: 3.94 Å

EMDB-15099: Consensus map of Complex I from Ovis aries at pH9, Closed state
手法: EM (単粒子) / 解像度: 3.9 Å

化合物

ChemComp-SF4:
IRON/SULFUR CLUSTER

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / FMN

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-CA:
Unknown entry / カルシウムジカチオン

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / DSPE / リン脂質*YM

ChemComp-UQ8:
Ubiquinone-8 / ユビキノン8

ChemComp-DCQ:
2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / デシルユビキノン

ChemComp-LFA:
EICOSANE / イコサン

ChemComp-HOH:
WATER

ChemComp-HQH:
Piericidin A / ピエリシジンA / 抗生剤*YM

ChemComp-C14:
TETRADECANE / テトラデカン

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / リン脂質*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 / AMP*YM

ChemComp-MYR:
MYRISTIC ACID / ミリスチン酸

ChemComp-K:
Unknown entry / カリウムカチオン

ChemComp-ZN:
Unknown entry

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

由来
  • escherichia coli (大腸菌)
  • escherichia coli bl21(de3) (大腸菌)
  • escherichia coli str. k-12 substr. mc4100 (大腸菌)
  • escherichia coliescherichia coli str. k-12 substr. mc4100 (大腸菌)
  • escherichia coli bl21 (大腸菌)
  • ovis aries (ヒツジ)
  • sheep (ヒツジ)
キーワードPROTON TRANSPORT / Complex I / NADH / Quinone / MEMBRANE PROTEIN / respiration / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase

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