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- EMDB-55048: CryoEM structure of NADH:quinone oxidoreductases YjlCD from Bacil... -

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Basic information

Entry
Database: EMDB / ID: EMD-55048
TitleCryoEM structure of NADH:quinone oxidoreductases YjlCD from Bacillus subtilis
Map dataCryoEM reconstruction of YjlCD from Bacillus subtilis
Sample
  • Complex: NAD(P)H:quinone oxidoreductases
    • Protein or peptide: NADH dehydrogenase-like protein YjlD
    • Protein or peptide: YjlC
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: HEPTANOIC ACID
  • Ligand: HEXANOIC ACID
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: PENTANOIC ACID
  • Ligand: GLYCEROL
  • Ligand: DECANOIC ACID
  • Ligand: water
KeywordsBacterial metabolism / Bioenergetics / Quinone / Helical Membrane Plug-in / OXIDOREDUCTASE
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
Uncharacterized protein YjlC / NADH dehydrogenase-like protein YjlD
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsOsman R / Cherrier MV / Nicolet Y / Juyoux P / Schoehn G / Seduk F / Garcia PS / Bizien-Jaglin L / Botte CY / Kosta A ...Osman R / Cherrier MV / Nicolet Y / Juyoux P / Schoehn G / Seduk F / Garcia PS / Bizien-Jaglin L / Botte CY / Kosta A / Lebrun R / Mate MJ / Pierrel F / Yamaryo-Botte Y / Walburger A / Magalon A
Funding support France, 7 items
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, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55048.png

Downloads & links

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Map

FileDownload / File: emd_55048.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of YjlCD from Bacillus subtilis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 500 pix.
= 290. Å		0.58 Å/pix.
x 500 pix.
= 290. Å		0.58 Å/pix.
x 500 pix.
= 290. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.068
Minimum - Maximum-0.5406209 - 0.90482867
Average (Standard dev.)0.00035077232 (±0.01750778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 290.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CryoEM reconstruction of YjlCD from Bacillus subtilis

Fileemd_55048_half_map_1.map
AnnotationCryoEM reconstruction of YjlCD from Bacillus subtilis
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM reconstruction of YjlCD from Bacillus subtilis

Fileemd_55048_half_map_2.map
AnnotationCryoEM reconstruction of YjlCD from Bacillus subtilis
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NAD(P)H:quinone oxidoreductases

EntireName: NAD(P)H:quinone oxidoreductases
Components
  • Complex: NAD(P)H:quinone oxidoreductases
    • Protein or peptide: NADH dehydrogenase-like protein YjlD
    • Protein or peptide: YjlC
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: HEPTANOIC ACID
  • Ligand: HEXANOIC ACID
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: PENTANOIC ACID
  • Ligand: GLYCEROL
  • Ligand: DECANOIC ACID
  • Ligand: water

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Supramolecule #1: NAD(P)H:quinone oxidoreductases

SupramoleculeName: NAD(P)H:quinone oxidoreductases / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 232 KDa

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Macromolecule #1: NADH dehydrogenase-like protein YjlD

MacromoleculeName: NADH dehydrogenase-like protein YjlD / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 42.002996 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: MSKHIVILGA GYGGVLSALT VRKHYTKEQA RVTVVNKYPT HQIITELHRL AAGNVSEKAV AMPLEKLFKG KDIDLKIAEV SSFSVDKKE VALADGSTLT YDALVVGLGS VTAYFGIPGL EENSMVLKSA ADANKVFQHV EDRVREYSKT KNEADATILI G GGGLTGVE ...String:
MSKHIVILGA GYGGVLSALT VRKHYTKEQA RVTVVNKYPT HQIITELHRL AAGNVSEKAV AMPLEKLFKG KDIDLKIAEV SSFSVDKKE VALADGSTLT YDALVVGLGS VTAYFGIPGL EENSMVLKSA ADANKVFQHV EDRVREYSKT KNEADATILI G GGGLTGVE LVGELADIMP NLAKKYGVDH KEIKLKLVEA GPKILPVLPD DLIERATASL EKRGVEFLTG LPVTNVEGNV ID LKDGSKV VANTFVWTGG VQGNPLVGES GLEVNRGRAT VNDFLQSTSH EDVFVAGDSA VYFGPDGRPY PPTAQIAWQM GEL IGYNLF AYLEGKTLET FKPVNSGTLA SLGRKDAVAI IGANSTPLKG LPASLMKEAS NVRYLTHIKG LFSLAY

UniProtKB: NADH dehydrogenase-like protein YjlD

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Macromolecule #2: YjlC

MacromoleculeName: YjlC / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 15.596558 KDa
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString:
MPETIDQTNA SVSQSQQDLI DQLLKPEVQE SLTVLVDQLP KLTELVNILT KSYDFAQSVA TDEVLKSDTV GAITEILEPV KETAKEVAA TAIEAKDRAE ASNETIGLFG LLRMLKDPQA QKLFRFANSY LEVMNERENQ K

UniProtKB: Uncharacterized protein YjlC

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Macromolecule #3: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 3 / Number of copies: 4 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #4: HEPTANOIC ACID

MacromoleculeName: HEPTANOIC ACID / type: ligand / ID: 4 / Number of copies: 20 / Formula: SHV
Molecular weightTheoretical: 130.185 Da
Chemical component information

ChemComp-SHV:
HEPTANOIC ACID

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Macromolecule #5: HEXANOIC ACID

MacromoleculeName: HEXANOIC ACID / type: ligand / ID: 5 / Number of copies: 16 / Formula: 6NA
Molecular weightTheoretical: 116.158 Da
Chemical component information

ChemComp-6NA:
HEXANOIC ACID

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Macromolecule #6: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 6 / Number of copies: 8 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM

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Macromolecule #7: PENTANOIC ACID

MacromoleculeName: PENTANOIC ACID / type: ligand / ID: 7 / Number of copies: 20 / Formula: LEA
Molecular weightTheoretical: 102.132 Da
Chemical component information

ChemComp-LEA:
PENTANOIC ACID

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Macromolecule #8: GLYCEROL

MacromoleculeName: GLYCEROL / type: ligand / ID: 8 / Number of copies: 28 / Formula: GOL
Molecular weightTheoretical: 92.094 Da
Chemical component information

ChemComp-GOL:
GLYCEROL

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Macromolecule #9: DECANOIC ACID

MacromoleculeName: DECANOIC ACID / type: ligand / ID: 9 / Number of copies: 8 / Formula: DKA
Molecular weightTheoretical: 172.265 Da
Chemical component information

ChemComp-DKA:
DECANOIC ACID

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 984 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6.25 mg/mL
BufferpH: 8
Component:
ConcentrationName
50.0 mMTris-HCl
150.0 mMNaCl
5.0 %Glycerol
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 43216 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4070805
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 691400
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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