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- PDB-7zc5: Complex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8... -

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Basic information

Entry
Database: PDB / ID: 7zc5
TitleComplex I from E. coli, DDM/LMNG-purified, under Turnover at pH 8, Resting state
Components
  • (NADH dehydrogenase I subunit ...) x 2
  • (NADH-quinone oxidoreductase subunit ...NADH dehydrogenase (quinone)) x 10
  • NADH-quinone oxidoreductaseNADH dehydrogenase (quinone)
KeywordsPROTON TRANSPORT / Complex I / NADH / Quinone
Function / homology
Function and homology information


plasma membrane respiratory chain complex I / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / 2 iron, 2 sulfur cluster binding ...plasma membrane respiratory chain complex I / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH:ubiquinone reductase (non-electrogenic) activity / respiratory chain complex I / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / 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
NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 ...NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / 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-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / 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, 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 / 4Fe-4S dicluster domain / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / EICOSANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit A ...1,2-Distearoyl-sn-glycerophosphoethanolamine / FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / EICOSANE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / IRON/SULFUR CLUSTER / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit E / : / : / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit H / :
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsKravchuk, V. / Kampjut, D. / Sazanov, L.
Funding support Austria, 1items
OrganizationGrant numberCountry
Not funded25541 Austria
CitationJournal: Nature / Year: 2022
Title: A universal coupling mechanism of respiratory complex I.
Authors: Vladyslav Kravchuk / Olga Petrova / Domen Kampjut / Anna Wojciechowska-Bason / Zara Breese / Leonid Sazanov /
Abstract: 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.
History
DepositionMar 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)551,25136
Polymers541,37513
Non-polymers9,87623
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area85630 Å2
ΔGint-835 kcal/mol
Surface area141260 Å2

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Components

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NADH-quinone oxidoreductase subunit ... , 10 types, 10 molecules FCBIHALNKJ

#1: Protein NADH-quinone oxidoreductase subunit F / NADH dehydrogenase (quinone)


Mass: 49352.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: A0A037YNA7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein NADH-quinone oxidoreductase subunit CD / NADH dehydrogenase (quinone)


Mass: 68810.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria) / References: UniProt: A0A839KEA0
#5: Protein NADH-quinone oxidoreductase subunit B / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit B / NDH-1 subunit B


Mass: 25081.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: E7T2M5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NADH-quinone oxidoreductase subunit I / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit I / NDH-1 subunit I


Mass: 20562.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: A0A4V1DR98, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#7: Protein NADH-quinone oxidoreductase subunit H / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit H / NDH-1 subunit H


Mass: 36240.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: E6BKM7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: Protein NADH-quinone oxidoreductase subunit A / NADH dehydrogenase (quinone) / 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 BL21 (bacteria)
References: UniProt: A0A358FP87, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#9: Protein NADH-quinone oxidoreductase subunit L / NADH dehydrogenase (quinone)


Mass: 66513.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: A0A1V3W1N5, NADH dehydrogenase (quinone)
#11: Protein NADH-quinone oxidoreductase subunit N / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit N / NDH-1 subunit N


Mass: 52072.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: E2QPD7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NADH-quinone oxidoreductase subunit K / NADH dehydrogenase (quinone) / NADH dehydrogenase I subunit K / NDH-1 subunit K


Mass: 10852.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: A0A7U9LRT0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#13: Protein NADH-quinone oxidoreductase subunit J / NADH dehydrogenase (quinone)


Mass: 19889.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria) / Strain: IAI39 / ExPEC
References: UniProt: A0A0H3MIP2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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NADH dehydrogenase I subunit ... , 2 types, 2 molecules EM

#2: Protein NADH dehydrogenase I subunit E / / NADH-quinone oxidoreductase subunit E / NDH-1 subunit E


Mass: 18614.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria) / References: UniProt: A0A829CRH1
#10: Protein NADH dehydrogenase I subunit M / / NADH-quinone oxidoreductase subunit M / NDH-1 subunit M


Mass: 56560.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria) / References: UniProt: C3T2G7

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Protein , 1 types, 1 molecules G

#3: Protein NADH-quinone oxidoreductase / NADH dehydrogenase (quinone)


Mass: 100349.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli BL21 (bacteria)
References: UniProt: A0A8A5GYF0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 7 types, 23 molecules

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


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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#16: 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
#17: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#18: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#19: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane


Mass: 282.547 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H42
#20: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM

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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: Complex IRespiratory complex I / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21-DE3
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
22 mMcalcium chlorideCaCl21
3250 mMsodium chlorideNaClSodium chloride1
40.01 %LMNGC47H88O221
50.25 mg/mlE. coli lipid extractC40H80NO8P1
60.1 %CHAPSC32H58N2O7S1
71.5 mMNADHNicotinamide adenine dinucleotideC21H27N7O14P21
80.75 mMDQC19H30O41
SpecimenConc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 288 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 magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8659
Image scansSampling size: 5 µm

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4092+SVNrefinement
PHENIXdev_4092+SVNrefinement
EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1648181
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82734 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: ML
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: 66.01 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006637607
ELECTRON MICROSCOPYf_angle_d0.837951030
ELECTRON MICROSCOPYf_chiral_restr0.05065710
ELECTRON MICROSCOPYf_plane_restr0.00696398
ELECTRON MICROSCOPYf_dihedral_angle_d12.64965467

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