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- PDB-9tak: Local refinement of E. coli Complex I WT membrane domain in LMNG -

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Basic information

Entry
Database: PDB / ID: 9tak
TitleLocal refinement of E. coli Complex I WT membrane domain in LMNG
Components(NADH-quinone oxidoreductase subunit ...) x 8
KeywordsPROTON TRANSPORT / bioenergetics
Function / homology
Function and homology information


NADH dehydrogenase (quinone) (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport ...NADH dehydrogenase (quinone) (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / 4 iron, 4 sulfur cluster binding / iron ion binding / membrane / plasma membrane
Similarity search - Function
NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / 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 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / 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. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / EICOSANE / TRIDECANE / Ubiquinone-8 / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K ...1,2-Distearoyl-sn-glycerophosphoethanolamine / CARDIOLIPIN / EICOSANE / TRIDECANE / Ubiquinone-8 / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit L
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKovalova, T. / Beghiah, A. / Kaila, V.R.I.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2024.0220 Sweden
Swedish Research Council2020-04081 Sweden
CitationJournal: To Be Published
Title: A Carboxylate Switch Point Controls Long-Range Energy Transduction in Respiratory Complex I
Authors: Beghiah, A. / Saura, P. / Kovalova, T. / Hoeser, F. / Friedrich, T. / Kaila, V.R.I.
History
DepositionNov 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: NADH-quinone oxidoreductase subunit H
J: NADH-quinone oxidoreductase subunit J
K: NADH-quinone oxidoreductase subunit K
M: NADH-quinone oxidoreductase subunit M
A: NADH-quinone oxidoreductase subunit A
B: NADH-quinone oxidoreductase subunit B
L: NADH-quinone oxidoreductase subunit L
N: NADH-quinone oxidoreductase subunit N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,66132
Polymers283,6568
Non-polymers16,00524
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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NADH-quinone oxidoreductase subunit ... , 8 types, 8 molecules HJKMABLN

#1: 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 genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoH, b2282, JW2277 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P0AFD4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: 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 genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoJ, b2280, JW2275 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P0AFE0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: 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 genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoK, b2279, JW2274 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P0AFE4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: 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 genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoM, b2277, JW2272 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P0AFE8, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: 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 genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoA, b2288, JW2283 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P0AFC3, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NADH-quinone oxidoreductase subunit B / NADH dehydrogenase I subunit B / NDH-1 subunit B / NUO2


Mass: 25081.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoB, b2287, JW5875 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P0AFC7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#7: Protein NADH-quinone oxidoreductase subunit L / NADH dehydrogenase I subunit L / NDH-1 subunit L / NUO12


Mass: 66483.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoL, b2278, JW2273 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P33607, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: 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 genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: nuoN, b2276, JW2271 / Production host: Escherichia coli BW25113 (bacteria)
References: UniProt: P0AFF0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Non-polymers , 6 types, 190 molecules

#9: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#10: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42
#11: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#12: Chemical ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H28
#13: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: NADH-quinone oxidoreductase, Complex I / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Source (recombinant)Organism: Escherichia coli BW25113 (bacteria)
Buffer solutionpH: 6
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70502 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003519729
ELECTRON MICROSCOPYf_angle_d0.601226612
ELECTRON MICROSCOPYf_chiral_restr0.03723013
ELECTRON MICROSCOPYf_plane_restr0.00343143
ELECTRON MICROSCOPYf_dihedral_angle_d18.1017345

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