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- PDB-9tao: Local refinement of E. coli Complex I D79N NuoA mutant membrane d... -

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Basic information

Entry
Database: PDB / ID: 9tao
TitleLocal refinement of E. coli Complex I D79N NuoA mutant membrane domain in LMNG
Components(NADH-quinone oxidoreductase subunit ...) x 7
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 / membrane / plasma membrane
Similarity search - Function
NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 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 ...NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 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
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Chem-7PH / CARDIOLIPIN / Ubiquinone-8 / NADH-quinone oxidoreductase subunit A / 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: 2.61 Å
AuthorsBeghiah, A. / Kovalova, T. / Kaila, V.R.I.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation2024.0220 Sweden
Swedish Research Council2020-04081 Sweden
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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
K: NADH-quinone oxidoreductase subunit K
L: NADH-quinone oxidoreductase subunit L
A: NADH-quinone oxidoreductase subunit A
J: NADH-quinone oxidoreductase subunit J
M: NADH-quinone oxidoreductase subunit M
N: NADH-quinone oxidoreductase subunit N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,29227
Polymers258,5737
Non-polymers14,71920
Water3,189177
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 ... , 7 types, 7 molecules HKLAJMN

#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 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
#3: 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
#4: Protein NADH-quinone oxidoreductase subunit A / NADH dehydrogenase I subunit A / NDH-1 subunit A / NUO1


Mass: 16473.299 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
#5: 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
#6: 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
#7: 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 , 5 types, 197 molecules

#8: 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.: 12 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#9: Chemical
ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID


Mass: 564.732 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C29H57O8P
#10: 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
#11: 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
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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-#7 / 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
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: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86927 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 22.82 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003319031
ELECTRON MICROSCOPYf_angle_d0.624425685
ELECTRON MICROSCOPYf_chiral_restr0.04142917
ELECTRON MICROSCOPYf_plane_restr0.00553033
ELECTRON MICROSCOPYf_dihedral_angle_d17.03847012

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