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- PDB-7nyv: Respiratory complex I from Escherichia coli - conformation 3 -

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Entry
Database: PDB / ID: 7nyv
TitleRespiratory complex I from Escherichia coli - conformation 3
Components(NADH-quinone oxidoreductase subunit ...) x 13
KeywordsELECTRON TRANSPORT / NADH:ubiquinone reductase (H+-translocating) / oxidative phosphorylation
Function / homology
Function and homology information


: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cellular respiration / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport ...: / NADH dehydrogenase complex / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cellular respiration / ubiquinone binding / NADH dehydrogenase activity / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / aerobic respiration / respiratory electron transport chain / proton transmembrane transport / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. ...NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / : / NADH-quinone oxidoreductase, subunit D / Aspartate decarboxylase-like domain superfamily / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit G
Similarity search - Component
Biological speciesEscherichia coli B (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKolata, P. / Efremov, R.G.
Funding support Belgium, 1items
OrganizationGrant numberCountry
European Research Council (ERC)00281ROEF Belgium
CitationJournal: Elife / Year: 2021
Title: Structure of respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation.
Authors: Piotr Kolata / Rouslan G Efremov /
Abstract: Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I ...Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I from is among the best functionally characterized complexes, but its structure remains unknown, hindering further studies to understand the enzyme coupling mechanism. Here, we describe the single particle cryo-electron microscopy (cryo-EM) structure of the entire catalytically active complex I reconstituted into lipid nanodiscs. The structure of this mesophilic bacterial complex I displays highly dynamic connection between the peripheral and membrane domains. The peripheral domain assembly is stabilized by unique terminal extensions and an insertion loop. The membrane domain structure reveals novel dynamic features. Unusual conformation of the conserved interface between the peripheral and membrane domains suggests an uncoupled conformation of the complex. Considering constraints imposed by the structural data, we suggest a new simple hypothetical coupling mechanism for the molecular machine.
History
DepositionMar 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
B: NADH-quinone oxidoreductase subunit B
D: NADH-quinone oxidoreductase subunit C/D
E: NADH-quinone oxidoreductase subunit E
F: NADH-quinone oxidoreductase subunit F
G: NADH-quinone oxidoreductase subunit G
I: NADH-quinone oxidoreductase subunit I
K: NADH-quinone oxidoreductase subunit K
J: NADH-quinone oxidoreductase subunit J
A: NADH-quinone oxidoreductase subunit A
H: NADH-quinone oxidoreductase subunit H
M: NADH-quinone oxidoreductase subunit M
L: NADH-quinone oxidoreductase subunit L
N: NADH-quinone oxidoreductase subunit N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)544,31424
Polymers541,00413
Non-polymers3,31011
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NADH-quinone oxidoreductase subunit ... , 13 types, 13 molecules BDEFGIKJAHMLN

#1: Protein NADH-quinone oxidoreductase subunit B / NADH dehydrogenase I subunit B / NDH-1 subunit B / NUO2


Mass: 25097.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFC7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase subunit C/D / NADH dehydrogenase I subunit C/D / NDH-1 subunit C/D / NUO3/NUO4


Mass: 68321.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P33599, NADH:ubiquinone reductase (H+-translocating)
#3: Protein NADH-quinone oxidoreductase subunit E


Mass: 18630.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFD1, NADH:ubiquinone reductase (H+-translocating)
#4: Protein NADH-quinone oxidoreductase subunit F


Mass: 49368.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P31979, NADH:ubiquinone reductase (H+-translocating)
#5: Protein NADH-quinone oxidoreductase subunit G


Mass: 100419.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P33602, NADH:ubiquinone reductase (H+-translocating)
#6: Protein NADH-quinone oxidoreductase subunit I


Mass: 20562.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFD6, NADH:ubiquinone reductase (H+-translocating)
#7: Protein NADH-quinone oxidoreductase subunit K / NADH dehydrogenase I subunit K / NDH-1 subunit K / NUO11


Mass: 10852.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFE4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: Protein NADH-quinone oxidoreductase subunit J / NADH dehydrogenase I subunit J / NDH-1 subunit J / NUO10


Mass: 19889.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFE0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#9: Protein NADH-quinone oxidoreductase subunit A / NADH dehydrogenase I subunit A / NDH-1 subunit A / NUO1


Mass: 16474.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFC3, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#10: Protein NADH-quinone oxidoreductase subunit H / NADH dehydrogenase I subunit H / NDH-1 subunit H / NUO8


Mass: 36240.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFD4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#11: Protein NADH-quinone oxidoreductase subunit M / NADH dehydrogenase I subunit M / NDH-1 subunit M / NUO13


Mass: 56560.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFE8, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NADH-quinone oxidoreductase subunit L / NuoL_2 protein


Mass: 66513.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: A0A1V3W1N5, NADH dehydrogenase (quinone), NADH:ubiquinone reductase (H+-translocating), NADH dehydrogenase (quinone)
#13: Protein NADH-quinone oxidoreductase subunit N / NADH dehydrogenase I subunit N / NDH-1 subunit N / NUO14


Mass: 52072.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI)
References: UniProt: P0AFF0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 4 types, 11 molecules

#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#16: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#17: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: Respiratory complex I from Escherichia coli - conformation 3
Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Molecular weightValue: 0.55 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli B (bacteria) / Strain: BL21(AI) / Cellular location: cell membrane
Buffer solutionpH: 6.8
Details: The buffer was used for gel filtration of protein reconstituted in lipid nanodiscs
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMBis-TrisC8H19NO51
2200 mMSodium chlorideNaCl1
32 mMCalcium chlorideCaCl21
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 97 % / Chamber temperature: 296 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm / Cs: 2.55 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 3 sec. / Electron dose: 64.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9122
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
7Coot0.9model fitting
9RELION3initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIX1.18.23D reconstruction
20PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1256734
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21234 / Symmetry type: POINT
Atomic model buildingB value: 93 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-ID
14HEA

4hea

1
23RKO

3rko

1
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 91.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00536089
ELECTRON MICROSCOPYf_angle_d0.850549117
ELECTRON MICROSCOPYf_chiral_restr0.04655554
ELECTRON MICROSCOPYf_plane_restr0.00626256
ELECTRON MICROSCOPYf_dihedral_angle_d13.97412664

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