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- PDB-9snk: CryoEM structure of NADH:quinone oxidoreductases YjlCD from Bacil... -

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Basic information

Entry
Database: PDB / ID: 9snk
TitleCryoEM structure of NADH:quinone oxidoreductases YjlCD from Bacillus subtilis
Components
  • NADH dehydrogenase-like protein YjlD
  • YjlC
KeywordsOXIDOREDUCTASE / Bacterial metabolism / Bioenergetics / Quinone / Helical Membrane Plug-in
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors / oxidoreductase activity
Similarity search - Function
Protein of unknown function DUF1641 / Helical membrane plugin / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / HEXANOIC ACID / DECANOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / PENTANOIC ACID / HEPTANOIC ACID / Uncharacterized protein YjlC / NADH dehydrogenase-like protein YjlD
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsOsman, R. / Cherrier, M.V. / Nicolet, Y. / Juyoux, P. / Schoehn, G. / Seduk, F. / Garcia, P.S. / Bizien-Jaglin, L. / Botte, C.Y. / Kosta, A. ...Osman, R. / Cherrier, M.V. / Nicolet, Y. / Juyoux, P. / Schoehn, G. / Seduk, F. / Garcia, P.S. / Bizien-Jaglin, L. / Botte, C.Y. / Kosta, A. / Lebrun, R. / Mate, M.J. / Pierrel, F. / Yamaryo-Botte, Y. / Walburger, A. / Magalon, A.
Funding support France, 7items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
Agence Nationale de la Recherche (ANR)ANR-21-ESRE-0046 France
Agence Nationale de la Recherche (ANR)ANR-23-CE15-0017 France
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0006 France
Fondation pour la Recherche Medicale (FRM) France
Region Auvergne Rhone Alpes France
CitationJournal: Nat Commun / Year: 2026
Title: A Bacillales-specific tubular scaffold essential for NADH dehydrogenase activity.
Authors: Seduk, F. / Osman, R. / Garcia, P.S. / Bizien-Jaglin, L. / Juyoux, P. / Kosta, A. / Sauvage, S. / Mate, M.J. / Pierrel, F. / Lebrun, R. / Schoehn, G. / Yamaryo-Botte, Y. / Botte, C.Y. / ...Authors: Seduk, F. / Osman, R. / Garcia, P.S. / Bizien-Jaglin, L. / Juyoux, P. / Kosta, A. / Sauvage, S. / Mate, M.J. / Pierrel, F. / Lebrun, R. / Schoehn, G. / Yamaryo-Botte, Y. / Botte, C.Y. / Nicolet, Y. / Cherrier, M.V. / Walburger, A. / Magalon, A.
History
DepositionSep 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 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

Downloads & links

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Assembly

Deposited unit
A: NADH dehydrogenase-like protein YjlD
B: YjlC
C: NADH dehydrogenase-like protein YjlD
D: YjlC
F: NADH dehydrogenase-like protein YjlD
G: YjlC
I: NADH dehydrogenase-like protein YjlD
J: YjlC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,987112
Polymers230,3988
Non-polymers19,588104
Water17,727984
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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Protein , 2 types, 8 molecules ACFIBDGJ

#1: Protein
NADH dehydrogenase-like protein YjlD / Glucose starvation-inducible protein 5 / GSI5


Mass: 42002.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yjlD, BSU12290
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: P80861, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Protein
YjlC


Mass: 15596.558 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: yjlC, BSU12280
Production host: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
References: UniProt: O34633

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Non-polymers , 8 types, 1088 molecules

#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical
ChemComp-SHV / HEPTANOIC ACID


Mass: 130.185 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C7H14O2
#5: Chemical
ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C6H12O2
#6: 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.: 8 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#7: Chemical
ChemComp-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C5H10O2
#8: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical
ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H20O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 984 / 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: NAD(P)H:quinone oxidoreductases / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.232 MDa / Experimental value: NO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (recombinant)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Buffer solutionpH: 8
Buffer component
IDConc.NameBuffer-ID
150 mMTris-HCl1
2150 mMNaCl1
35 %Glycerol1
SpecimenConc.: 6.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 30 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 2900 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 43216
EM imaging opticsEnergyfilter name: TFS Selectris X / Phase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.1particle selection
2EPUimage acquisition
4cryoSPARC4.5.1CTF correction
10cryoSPARC4.5.1initial Euler assignment
11cryoSPARC4.5.1final Euler assignment
12cryoSPARC4.5.1classification
13cryoSPARC4.5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4070805
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 691400 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT

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