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- EMDB-71972: CryoEM structure of Ndh-Ncp complex from Bacillus subtilis with N... -

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Basic information

Entry
Database: EMDB / ID: EMD-71972
TitleCryoEM structure of Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8
Map data
Sample
  • Complex: Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8
    • Protein or peptide: NADH dehydrogenase-like protein YjlD
    • Protein or peptide: NDH-2 membrane coupling protein
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: MENAQUINONE 8
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
KeywordsNADH dehydrogenase / respiratory protein / FLAVOPROTEIN / protein complex / enzyme
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: 2.52 Å
AuthorsKropp A / Grinter R
Funding support Australia, 1 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230103080 Australia
CitationJournal: To Be Published
Title: Long-range quinone transport couples NADH oxidation to the respiratory chain in Bacillota
Authors: Kropp A / Stapleton J / Zdorevskyi O / Leung PM / Darnell R / Barlow C / Hartmann B / Yates N / Simsive L / Asadollahi K / Sharma V / Greening C / Blaza J / Parkin A / Grinter R
History
DepositionAug 5, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71972.png

Downloads & links

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Map

FileReleased
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 420 pix.
= 339.36 Å		0.81 Å/pix.
x 420 pix.
= 339.36 Å		0.81 Å/pix.
x 420 pix.
= 339.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.135
Minimum - Maximum-0.29621047 - 1.0717523
Average (Standard dev.)0.0005252599 (±0.020506687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 339.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71972_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71972_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8

EntireName: Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8
Components
  • Complex: Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8
    • Protein or peptide: NADH dehydrogenase-like protein YjlD
    • Protein or peptide: NDH-2 membrane coupling protein
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: MENAQUINONE 8
  • Ligand: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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Supramolecule #1: Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8

SupramoleculeName: Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)

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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: Escherichia coli (E. coli)
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: NDH-2 membrane coupling protein

MacromoleculeName: NDH-2 membrane coupling protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 19.408564 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
WSHPQFEKGG GSGGGSGGSA WSHPQFEKEN LYFQGSMPET IDQTNASVSQ SQQDLIDQLL KPEVQESLTV LVDQLPKLTE LVNILTKSY DFAQSVATDE VLKSDTVGAI TEILEPVKET AKEVAATAIE AKDRAEASNE TIGLFGLLRM LKDPQAQKLF R FANSYLEV MNERENQK

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: MENAQUINONE 8

MacromoleculeName: MENAQUINONE 8 / type: ligand / ID: 4 / Number of copies: 4 / Formula: MQ8
Molecular weightTheoretical: 717.116 Da
Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

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Macromolecule #5: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

MacromoleculeName: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / type: ligand / ID: 5 / Number of copies: 4 / Formula: NAI
Molecular weightTheoretical: 665.441 Da
Chemical component information

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

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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

Concentration5 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMSodium chlorideNaCl
GridModel: UltrAuFoil / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 96000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2723185
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 341297
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9pxk:
CryoEM structure of Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8

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