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- PDB-9pxk: CryoEM structure of Ndh-Ncp complex from Bacillus subtilis with N... -

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Basic information

Entry
Database: PDB / ID: 9pxk
TitleCryoEM structure of Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8
Components
  • NADH dehydrogenase-like protein YjlD
  • NDH-2 membrane coupling protein
KeywordsFLAVOPROTEIN / NADH dehydrogenase / respiratory protein / 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
FLAVIN-ADENINE DINUCLEOTIDE / MENAQUINONE 8 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 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: 2.52 Å
AuthorsKropp, A. / Grinter, R.
Funding support Australia, 1items
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, P.M. / 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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: NADH dehydrogenase-like protein YjlD
E: NDH-2 membrane coupling protein
F: NDH-2 membrane coupling protein
G: NDH-2 membrane coupling protein
H: NDH-2 membrane coupling protein
A: NADH dehydrogenase-like protein YjlD
B: NADH dehydrogenase-like protein YjlD
D: NADH dehydrogenase-like protein YjlD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,31920
Polymers245,6468
Non-polymers8,67212
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#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: Escherichia coli (E. coli)
References: UniProt: P80861, Oxidoreductases; Acting on NADH or NADPH; With unknown physiological acceptors
#2: Protein
NDH-2 membrane coupling protein


Mass: 19408.564 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: Escherichia coli (E. coli) / References: UniProt: O34633
#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-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H72O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
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: Ndh-Ncp complex from Bacillus subtilis with NADH and MK-8
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: 96000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
5cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2723185
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 341297 / Symmetry type: POINT
Atomic model building
ID
1
2
Atomic model building
ID 3D fitting-IDSource nameType
11AlphaFoldin silico model
22
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216420
ELECTRON MICROSCOPYf_angle_d0.50822308
ELECTRON MICROSCOPYf_dihedral_angle_d11.6552304
ELECTRON MICROSCOPYf_chiral_restr0.0482596
ELECTRON MICROSCOPYf_plane_restr0.0042804

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