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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: Farida Seduk / Rayan Osman / Pierre Simon Garcia / Lilou Bizien-Jaglin / Pauline Juyoux / Artemis Kosta / Salomé Sauvage / Maria J Maté / Fabien Pierrel / Régine Lebrun / Guy Schoehn / ...Authors: Farida Seduk / Rayan Osman / Pierre Simon Garcia / Lilou Bizien-Jaglin / Pauline Juyoux / Artemis Kosta / Salomé Sauvage / Maria J Maté / Fabien Pierrel / Régine Lebrun / Guy Schoehn / Yoshiki Yamaryo-Botté / Cyrille Y Botté / Yvain Nicolet / Mickael V Cherrier / Anne Walburger / Axel Magalon /
Abstract: Respiratory type II NADH:quinone oxidoreductases (NDH-II) are typically monotopic flavoproteins that make direct contact with the membrane to access the quinone pool. Here, we show that in Bacillus ...Respiratory type II NADH:quinone oxidoreductases (NDH-II) are typically monotopic flavoproteins that make direct contact with the membrane to access the quinone pool. Here, we show that in Bacillus subtilis, one NDH-II, termed Ndh, assembles with the helical membrane plugin (HMP) protein YjlC and forms supramolecular fibers. Genetic and biochemical analyses demonstrate that Ndh and YjlC proteins are essential for NADH oxidation. Cryo-EM analysis reveals that YjlC forms a tubular scaffold onto which multiple Ndh subunits are regularly docked via their C-terminal domain, repurposed from its classical role in direct membrane binding. These fibers can extend up to ~1000 Å, creating a continuous hydrophobic tunnel filled with lipids and quinones, thereby mimicking the membrane environment. Comparative genomics unveils that this partnership arose exclusively within Bacillales through the recruitment of an ancestral HMP originally associated with sulfide:quinone reductases. Together, our findings uncover a lineage-specific structural adaptation in which NDH-II enzymes depend on an HMP scaffold, expanding their functional diversity beyond the classical monotopic paradigm.
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
Revision 1.1Aug 12, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

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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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