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- PDB-6zk9: Peripheral domain of open complex I during turnover -

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Entry
Database: PDB / ID: 6zk9
TitlePeripheral domain of open complex I during turnover
Components
  • (Mitochondrial complex I, ...Respiratory complex I) x 9
  • (NADH dehydrogenase [ubiquinone] ...) x 4
  • (NADH:ubiquinone oxidoreductase core subunit ...) x 2
  • (NADH:ubiquinone oxidoreductase subunit ...) x 2
  • Acyl carrier protein
KeywordsELECTRON TRANSPORT / complex / respiration / NADH / proton pump / mitochondria / iron-sulphur cluster / oxidoreductase / membrane protein
Function / homology
Function and homology information


blastocyst hatching / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport ...blastocyst hatching / NADH dehydrogenase activity / NADH:ubiquinone reductase (H+-translocating) / cellular respiration / protein lipoylation / mitochondrial respiratory chain complex I / mitochondrial ATP synthesis coupled electron transport / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / ATP synthesis coupled electron transport / NADH dehydrogenase (ubiquinone) activity / mitochondrial large ribosomal subunit / apoptotic mitochondrial changes / reactive oxygen species metabolic process / respirasome / respiratory electron transport chain / negative regulation of intrinsic apoptotic signaling pathway / response to cAMP / regulation of mitochondrial membrane potential / regulation of protein phosphorylation / 2 iron, 2 sulfur cluster binding / positive regulation of fibroblast proliferation / mitochondrial intermembrane space / negative regulation of cell growth / circadian rhythm / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / FMN binding / brain development / mitochondrial inner membrane / response to oxidative stress / nuclear body / mitochondrial matrix / oxidoreductase activity / protein-containing complex binding / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
2Fe-2S iron-sulfur cluster binding domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Thioredoxin-like [2Fe-2S] ferredoxin / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 ...2Fe-2S iron-sulfur cluster binding domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / Thioredoxin-like [2Fe-2S] ferredoxin / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH:ubiquinone oxidoreductase, subunit G / NADH ubiquinone oxidoreductase, F subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NuoE domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH dehydrogenase, subunit C / Soluble ligand binding domain / NADH-quinone oxidoreductase subunit E-like / SLBB domain / NADH-quinone oxidoreductase subunit E, N-terminal / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / Complex 1 protein (LYR family) / Complex 1 LYR protein domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Complex I-B14.5a / Acyl carrier protein / Complex I-30kD / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH:ubiquinone oxidoreductase subunit A9 / Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial ...Complex I-B14.5a / Acyl carrier protein / Complex I-30kD / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH:ubiquinone oxidoreductase subunit A9 / Complex I subunit B13 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / 1,2-Distearoyl-sn-glycerophosphoethanolamine / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / CARDIOLIPIN / Chem-ZMP / IRON/SULFUR CLUSTER / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-NDP / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / : / FLAVIN MONONUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / Complex I-B14
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsKampjut, D. / Sazanov, L.A.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Commission665385European Union
European Commission653706European Union
CitationJournal: Science / Year: 2020
Title: The coupling mechanism of mammalian respiratory complex I.
Authors: Domen Kampjut / Leonid A Sazanov /
Abstract: 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 ...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.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume

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Assembly

Deposited unit
1: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
2: Mitochondrial complex I, 24 kDa subunit
3: NADH:ubiquinone oxidoreductase core subunit S1
4: Mitochondrial complex I, 49 kDa subunit
5: NADH:ubiquinone oxidoreductase core subunit S3
6: Mitochondrial complex I, PSST subunit
9: Mitochondrial complex I, TYKY subunit
a: Mitochondrial complex I, 10 kDa subunit
b: Mitochondrial complex I, 13 kDa subunit
c: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
d: NADH:ubiquinone oxidoreductase subunit A9
e: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
f: Mitochondrial complex I, B13 subunit
g: NADH:ubiquinone oxidoreductase subunit A6
h: Mitochondrial complex I, B14.5a subunit
i: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
j: Acyl carrier protein
q: Mitochondrial complex I, B16.6 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,94937
Polymers482,40718
Non-polymers9,54219
Water26,5181472
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100660 Å2
ΔGint-522 kcal/mol
Surface area111690 Å2
MethodPISA

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Components

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NADH dehydrogenase [ubiquinone] ... , 4 types, 4 molecules 1cei

#1: Protein NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial


Mass: 50687.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
References: UniProt: W5PUX0, NADH dehydrogenase, NADH:ubiquinone reductase (H+-translocating)
#10: Protein NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Complex I-18 kDa / NADH-ubiquinone oxidoreductase 18 kDa subunit


Mass: 19381.994 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PE07
#12: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2


Mass: 11097.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QAH8
#16: Protein NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12


Mass: 17115.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: B9VGZ9

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Mitochondrial complex I, ... , 9 types, 9 molecules 2469abfhq

#2: Protein Mitochondrial complex I, 24 kDa subunit


Mass: 27373.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NRY1
#4: Protein Mitochondrial complex I, 49 kDa subunit


Mass: 52661.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#6: Protein Mitochondrial complex I, PSST subunit


Mass: 24622.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#7: Protein Mitochondrial complex I, TYKY subunit


Mass: 24496.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#8: Protein Mitochondrial complex I, 10 kDa subunit


Mass: 11916.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#9: Protein Mitochondrial complex I, 13 kDa subunit


Mass: 13457.175 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)
#13: Protein Mitochondrial complex I, B13 subunit


Mass: 13287.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PNX7
#15: Protein Mitochondrial complex I, B14.5a subunit


Mass: 12701.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P0I2
#18: Protein Mitochondrial complex I, B16.6 subunit


Mass: 16766.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep)

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NADH:ubiquinone oxidoreductase core subunit ... , 2 types, 2 molecules 35

#3: Protein NADH:ubiquinone oxidoreductase core subunit S1


Mass: 79519.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QB34
#5: Protein NADH:ubiquinone oxidoreductase core subunit S3


Mass: 30384.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PB27

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NADH:ubiquinone oxidoreductase subunit ... , 2 types, 2 molecules dg

#11: Protein NADH:ubiquinone oxidoreductase subunit A9 /


Mass: 43025.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PI58
#14: Protein NADH:ubiquinone oxidoreductase subunit A6 /


Mass: 16302.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5QC06

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Protein , 1 types, 1 molecules j

#17: Protein Acyl carrier protein /


Mass: 17608.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NQT7

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Non-polymers , 12 types, 1491 molecules

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


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#20: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#21: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#22: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#23: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#24: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#25: Chemical ChemComp-3PE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / 3-SN-PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#26: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#27: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#28: Chemical ChemComp-ZMP / S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate


Mass: 568.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H49N2O8PS
#29: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#30: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1472 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Peripheral domain of open complex I during turnover / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Ovis aries (sheep)
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 100 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4.15CTF correction
7Coot0.8.9model fitting
9PHENIX1.12model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315484 / Symmetry type: POINT
Atomic model buildingB value: 38 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5LNK
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00828783
ELECTRON MICROSCOPYf_angle_d1.39839031
ELECTRON MICROSCOPYf_dihedral_angle_d11.11117546
ELECTRON MICROSCOPYf_chiral_restr0.0674220
ELECTRON MICROSCOPYf_plane_restr0.0075031

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