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- PDB-6ziy: Respiratory complex I from Thermus thermophilus, NADH dataset, ma... -

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Entry
Database: PDB / ID: 6ziy
TitleRespiratory complex I from Thermus thermophilus, NADH dataset, major state
Components(NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 15
KeywordsMEMBRANE PROTEIN / Respiratory chain / complex I / NADH:ubiquinone oxidoreductase / electron transfer / proton translocation
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) activity / respiratory chain complex I / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / iron-sulfur cluster assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) activity / respiratory chain complex I / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / iron-sulfur cluster assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / ferric iron binding / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / plasma membrane
Similarity search - Function
NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / 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 / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain ...NADH-quinone oxidoreductase, subunit15 / NADH-quinone oxidoreductase, subunit 15 superfamily / NADH-quinone oxidoreductase chain 15 / Frataxin/CyaY superfamily / 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 / 4Fe-4S binding domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB domain / 2Fe-2S iron-sulfur cluster binding domain / Cro/C1-type helix-turn-helix domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NuoE domain / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Aspartate decarboxylase-like domain superfamily / 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 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 ...FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit 7 / NADH-quinone oxidoreductase subunit 6 / NADH-quinone oxidoreductase subunit 5 / NADH-quinone oxidoreductase subunit 4 / NADH-quinone oxidoreductase subunit 2 / NADH-quinone oxidoreductase subunit 1 / NADH-quinone oxidoreductase subunit 3 / NADH-quinone oxidoreductase subunit 9 / NADH-quinone oxidoreductase subunit 10 / NADH-quinone oxidoreductase subunit 11 / NADH-quinone oxidoreductase subunit 12 / NADH-quinone oxidoreductase subunit 13 / NADH-quinone oxidoreductase subunit 14 / NADH-quinone oxidoreductase subunit 15 / NADH-quinone oxidoreductase subunit 8
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsKaszuba, K. / Tambalo, M. / Gallagher, G.T. / Sazanov, L.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105674180 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Key role of quinone in the mechanism of respiratory complex I.
Authors: Javier Gutiérrez-Fernández / Karol Kaszuba / Gurdeep S Minhas / Rozbeh Baradaran / Margherita Tambalo / David T Gallagher / Leonid A Sazanov /
Abstract: Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in ...Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
History
DepositionJun 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
1: NADH-quinone oxidoreductase subunit 1
2: NADH-quinone oxidoreductase subunit 2
3: NADH-quinone oxidoreductase subunit 3
4: NADH-quinone oxidoreductase subunit 4
5: NADH-quinone oxidoreductase subunit 5
6: NADH-quinone oxidoreductase subunit 6
9: NADH-quinone oxidoreductase subunit 9
7: NADH-quinone oxidoreductase subunit 15
A: NADH-quinone oxidoreductase subunit 7
J: NADH-quinone oxidoreductase subunit 10
K: NADH-quinone oxidoreductase subunit 11
L: NADH-quinone oxidoreductase subunit 12
M: NADH-quinone oxidoreductase subunit 13
N: NADH-quinone oxidoreductase subunit 14
H: NADH-quinone oxidoreductase subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)526,75226
Polymers522,81815
Non-polymers3,93511
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area87980 Å2
ΔGint-799 kcal/mol
Surface area143400 Å2
MethodPISA

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Components

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NADH-quinone oxidoreductase subunit ... , 15 types, 15 molecules 12345697AJKLMNH

#1: Protein NADH-quinone oxidoreductase subunit 1 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 1 / NDH-1 subunit 1


Mass: 48693.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56222, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NADH-quinone oxidoreductase subunit 2 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 2 / NDH-1 subunit 2


Mass: 20309.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56221, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein NADH-quinone oxidoreductase subunit 3 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 3 / NDH-1 subunit 3


Mass: 86656.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56223, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein NADH-quinone oxidoreductase subunit 4 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 4 / NDH-1 subunit 4


Mass: 46428.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56220, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein NADH-quinone oxidoreductase subunit 5 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 5 / NDH-1 subunit 5


Mass: 23893.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56219, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NADH-quinone oxidoreductase subunit 6 / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit 6 / NDH-1 subunit 6


Mass: 20262.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56218, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#7: Protein NADH-quinone oxidoreductase subunit 9 / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit 9 / NDH-1 subunit 9


Mass: 20106.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56224, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: Protein NADH-quinone oxidoreductase subunit 15 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 15 / NDH-1 subunit 15


Mass: 14812.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q5SKZ7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#9: Protein NADH-quinone oxidoreductase subunit 7 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 7 / NDH-1 subunit 7


Mass: 13154.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56217, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#10: Protein NADH-quinone oxidoreductase subunit 10 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 10 / NDH-1 subunit 10


Mass: 18563.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56225, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#11: Protein NADH-quinone oxidoreductase subunit 11 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 11 / NDH-1 subunit 11


Mass: 10002.788 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56226, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NADH-quinone oxidoreductase subunit 12 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 12 / NDH-1 subunit 12


Mass: 65189.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56227, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#13: Protein NADH-quinone oxidoreductase subunit 13 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 13 / NDH-1 subunit 13


Mass: 49247.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56228, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#14: Protein NADH-quinone oxidoreductase subunit 14 / NADH dehydrogenase (quinone) / NADH dehydrogenase I chain 14 / NDH-1 subunit 14


Mass: 44463.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q56229, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#15: Protein NADH-quinone oxidoreductase subunit 8 / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit 8 / NDH-1 subunit 8


Mass: 41034.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria)
References: UniProt: Q60019, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 4 types, 11 molecules

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


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#17: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#18: 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
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2

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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 Thermus thermophilus / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Molecular weightValue: 0.53 MDa / Experimental value: NO
Source (natural)Organism: Thermus thermophilus (bacteria) / Strain: HB8
Buffer solutionpH: 6
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: with 5 mM NADH
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 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 / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 34 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 2184
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096 / Movie frames/image: 34 / Used frames/image: 1-34

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFINDCTF correction
7MDFFmodel fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13MDFFmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 205000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44500 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6Y11

6y11

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