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- PDB-12ke: Mycobacterial NDH-2 (type II NADH:quinone oxidoreductase) with tr... -

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Basic information

Entry
Database: PDB / ID: 12ke
TitleMycobacterial NDH-2 (type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
ComponentsNADH:ubiquinone reductase (non-electrogenic)
KeywordsMEMBRANE PROTEIN / Oxidoreductase / metabolism / flavoprotein / bioenergetics
Function / homology
Function and homology information


NADH dehydrogenase (menaquinone) (non-electrogenic) activity / NADH:quinone reductase (non-electrogenic) / plasma membrane
Similarity search - Function
Alternative NADH dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / NADH:ubiquinone reductase (non-electrogenic)
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLiang, Y. / Rubinstein, J.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: To Be Published
Title: Mycobacterial NDH-2 (type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
Authors: Liang, Y. / Rubinstein, J.L.
History
DepositionApr 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH:ubiquinone reductase (non-electrogenic)
B: NADH:ubiquinone reductase (non-electrogenic)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3546
Polymers106,6452
Non-polymers2,7084
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein NADH:ubiquinone reductase (non-electrogenic)


Mass: 53322.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the tagged sequence was inserted into the genome, the protein we purified is still under the control of the endogenous promoter and is the original gene in the genome
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: ndh, MSMEG_3621
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: A0QYD6, NADH:quinone reductase (non-electrogenic)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-A1DCJ / (3S,4R,7aR,9S,11aR)-9-(bis{[4-(trifluoromethyl)phenyl]methyl}amino)-3-(propan-2-yl)octahydro[1,3]oxazolo[2,3-j]quinolin-5(6H)-one / tricyclic spirolactam inhibitor


Mass: 568.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H34F6N2O2 / 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: Mycobacterial NDH-2 ((type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.049 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 286 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: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv5.0.0-betaparticle selection
2PHENIX1.19.2_4158model refinement
5cryoSPARCv5.0.0-betaCTF correction
10cryoSPARCv5.0.0-betainitial Euler assignment
11cryoSPARCv5.0.0-betafinal Euler assignment
13cryoSPARCv5.0.0-beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62351 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037070
ELECTRON MICROSCOPYf_angle_d0.5699616
ELECTRON MICROSCOPYf_dihedral_angle_d8.778988
ELECTRON MICROSCOPYf_chiral_restr0.0441104
ELECTRON MICROSCOPYf_plane_restr0.0041210

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