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Structure paper

TitleThe coupling mechanism of mammalian respiratory complex I.
Journal, issue, pagesScience, Vol. 370, Issue 6516, Year 2020
Publish dateOct 30, 2020
AuthorsDomen Kampjut / Leonid A Sazanov /
PubMed AbstractMitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different ...Mitochondrial complex I couples NADH:ubiquinone oxidoreduction to proton pumping by an unknown mechanism. Here, we present cryo-electron microscopy structures of ovine complex I in five different conditions, including turnover, at resolutions up to 2.3 to 2.5 angstroms. Resolved water molecules allowed us to experimentally define the proton translocation pathways. Quinone binds at three positions along the quinone cavity, as does the inhibitor rotenone that also binds within subunit ND4. Dramatic conformational changes around the quinone cavity couple the redox reaction to proton translocation during open-to-closed state transitions of the enzyme. In the induced deactive state, the open conformation is arrested by the ND6 subunit. We propose a detailed molecular coupling mechanism of complex I, which is an unexpected combination of conformational changes and electrostatic interactions.
External linksScience / PubMed:32972993
MethodsEM (single particle)
Resolution2.3 - 3.8 Å
Structure data

EMDB-11241, PDB-6zk9:
Peripheral domain of open complex I during turnover
Method: EM (single particle) / Resolution: 2.3 Å

EMDB-11242, PDB-6zka:
Membrane domain of open complex I during turnover
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-11243, PDB-6zkb:
Membrane domain of closed complex I during turnover
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-11244, PDB-6zkc:
Complex I during turnover, closed
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-11245, PDB-6zkd:
Complex I during turnover, open1
Method: EM (single particle) / Resolution: 2.7 Å

EMDB-11246, PDB-6zke:
Complex I during turnover, open2
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-11247, PDB-6zkf:
Complex I during turnover, open3
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-11248, PDB-6zkg:
Complex I with NADH, closed
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-11249, PDB-6zkh:
Complex I with NADH, open1
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-11250, PDB-6zki:
Complex I with NADH, open2
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-11251, PDB-6zkj:
Complex I with NADH, open3
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-11252, PDB-6zkk:
Complex I inhibited by rotenone, closed
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-11253, PDB-6zkl:
Complex I inhibited by rotenone, open1
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-11254, PDB-6zkm:
Complex I inhibited by rotenone, open2
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-11255, PDB-6zkn:
Complex I inhibited by rotenone, open3
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-11256, PDB-6zko:
Native complex I, closed
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-11257, PDB-6zkp:
Native complex I, open1
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-11258, PDB-6zkq:
Native complex I, open2
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-11259, PDB-6zkr:
Native complex I, open3
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-11260, PDB-6zks:
Deactive complex I, open1
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-11261, PDB-6zkt:
Deactive complex I, open2
Method: EM (single particle) / Resolution: 2.8 Å

EMDB-11262, PDB-6zku:
Deactive complex I, open3
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-11263, PDB-6zkv:
Deactive complex I, open4
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-15216: Complex I inhibited by rotenone open3
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

ChemComp-K:
Unknown entry

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

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

ChemComp-ZN:
Unknown entry

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

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

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

ChemComp-HOH:
WATER / Water

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

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM / Adenosine monophosphate

ChemComp-MYR:
MYRISTIC ACID / Myristic acid

ChemComp-970:
(2R,6aS,12aS)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12,12a-tetrahydrofuro[2',3':7,8][1]benzopyrano[2,3-c][1]benzopyran-6(6aH)-one / Rotenone

Source
  • ovis aries (sheep)
  • Sheep (sheep)
KeywordsELECTRON TRANSPORT / complex / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein

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