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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
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: Seduk F / Osman R / Garcia PS / Bizien-Jaglin L / Juyoux P / Kosta A / Sauvage S / Mate MJ / Pierrel F / Lebrun R / Schoehn G / Yamaryo-Botte Y / Botte CY / Nicolet Y / Cherrier MV / Walburger A / Magalon A
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_55048.png

Downloads & links

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Map

FileReleased
AnnotationCryoEM reconstruction of YjlCD from Bacillus subtilis
Voxel sizeX=Y=Z: 0.58 Å
Density
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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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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