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- EMDB-55049: CryoEM structure of NADH:quinone oxidoreductases YjlCD fiber's HM... -

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Basic information

Entry
Database: EMDB / ID: EMD-55049
TitleCryoEM structure of NADH:quinone oxidoreductases YjlCD fiber's HMP extremity from Bacillus subtilis
Map dataCryoEM reconstruction of YjlCD fiber's HMP extremity from Bacillus subtilis
Sample
  • Complex: NAD(P)H:quinone oxidoreductases
    • Protein or peptide: NAD(P)/FAD-dependent oxidoreductase - YjlD
    • Protein or peptide: YjlC
KeywordsBacterial metabolism / Bioenergetics / Quinone / Helical Membrane Plug-in / OXIDOREDUCTASE
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 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-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55049.png

Downloads & links

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Map

FileDownload / File: emd_55049.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of YjlCD fiber's HMP extremity 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: 0.0337
Minimum - Maximum-0.19407754 - 0.31000358
Average (Standard dev.)0.0006139975 (±0.0119888075)
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 fiber's HMP extremity from...

Fileemd_55049_half_map_1.map
AnnotationCryoEM reconstruction of YjlCD fiber's HMP extremity 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 fiber's HMP extremity from...

Fileemd_55049_half_map_2.map
AnnotationCryoEM reconstruction of YjlCD fiber's HMP extremity 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: NAD(P)/FAD-dependent oxidoreductase - YjlD
    • Protein or peptide: YjlC

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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: all
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 232 KDa

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Macromolecule #1: NAD(P)/FAD-dependent oxidoreductase - YjlD

MacromoleculeName: NAD(P)/FAD-dependent oxidoreductase - YjlD / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString: MSKHIVILGA GYGGVLSALT VRKHYTKEQA RVTVVNKYPT HQIITELHRL AAGNVSEKAV AMPLEKLFKG KDIDLKIAE VSSFSVDKKE VALADGSTLT YDALVVGLGS VTAYFGIPGL EENSMVLKSA ADANKVFQHV E DRVREYSK TKNEADATIL IGGGGLTGVE ...String:
MSKHIVILGA GYGGVLSALT VRKHYTKEQA RVTVVNKYPT HQIITELHRL AAGNVSEKAV AMPLEKLFKG KDIDLKIAE VSSFSVDKKE VALADGSTLT YDALVVGLGS VTAYFGIPGL EENSMVLKSA ADANKVFQHV E DRVREYSK TKNEADATIL IGGGGLTGVE LVGELADIMP NLAKKYGVDH KEIKLKLVEA GPKILPVLPD DL IERATAS LEKRGVEFLT GLPVTNVEGN VIDLKDGSKV VANTFVWTGG VQGNPLVGES GLEVNRGRAT VND FLQSTS HEDVFVAGDS AVYFGPDGRP YPPTAQIAWQ MGELIGYNLF AYLEGKTLET FKPVNSGTLA SLGR KDAVA IIGANSTPLK GLPASLMKEA SNVRYLTHIK GLFSLAY

UniProtKB: NADH dehydrogenase-like protein YjlD

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Macromolecule #2: YjlC

MacromoleculeName: YjlC / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Recombinant expressionOrganism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
SequenceString:
MPETIDQTNA SVSQSQQDLI DQLLKPEVQE SLTVLVDQLP KLTELVNILT KSYDFAQSVA TDEVLKSDTV GAITEILEPV KETAKEVAAT AIEAKDRAEA SNETIGLFGL LRMLKDPQAQ KLFRFANSYL EVMNERENQK

UniProtKB: Uncharacterized protein YjlC

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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: 42508
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 4133
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: 3 / Software - Name: cryoSPARC (ver. 4.5.1)
FSC plot (resolution estimation)

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