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- EMDB-76509: Mycobacterial NDH-2 (type II NADH:quinone oxidoreductase) with tr... -

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Basic information

Entry
Database: EMDB / ID: EMD-76509
TitleMycobacterial NDH-2 (type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
Map data
Sample
  • Complex: Mycobacterial NDH-2 ((type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
    • Protein or peptide: NADH:ubiquinone reductase (non-electrogenic)
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: (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
KeywordsOxidoreductase / metabolism / flavoprotein / bioenergetics / MEMBRANE PROTEIN
Function / homologyNADH dehydrogenase (menaquinone) (non-electrogenic) activity / Alternative NADH dehydrogenase / NADH:quinone reductase (non-electrogenic) / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / plasma membrane / NADH:ubiquinone reductase (non-electrogenic)
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiang Y / Rubinstein JL
Funding support Canada, 1 items
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 JL
History
DepositionApr 9, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76509.png

Downloads & links

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Map

FileDownload / File: emd_76509.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 288 pix.
= 210.24 Å		0.73 Å/pix.
x 288 pix.
= 210.24 Å		0.73 Å/pix.
x 288 pix.
= 210.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0406
Minimum - Maximum-0.15370062 - 0.34214267
Average (Standard dev.)0.0015195934 (±0.0114089595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 210.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map

Fileemd_76509_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76509_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76509_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterial NDH-2 ((type II NADH:quinone oxidoreductase) with t...

EntireName: Mycobacterial NDH-2 ((type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
Components
  • Complex: Mycobacterial NDH-2 ((type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
    • Protein or peptide: NADH:ubiquinone reductase (non-electrogenic)
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: (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

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Supramolecule #1: Mycobacterial NDH-2 ((type II NADH:quinone oxidoreductase) with t...

SupramoleculeName: Mycobacterial NDH-2 ((type II NADH:quinone oxidoreductase) with tricyclic spirolactam inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 49 KDa

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

MacromoleculeName: NADH:ubiquinone reductase (non-electrogenic) / type: protein_or_peptide / ID: 1
Details: Affinity tagging sequence directly introduced to the genomic dna of the source organism.
Number of copies: 2 / Enantiomer: LEVO / EC number: NADH:quinone reductase (non-electrogenic)
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) / Strain: ATCC 700084 / mc(2)155
Molecular weightTheoretical: 53.322723 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MSHPGATASD RHKVVIIGSG FGGLTAAKTL KRADVDVKLI ARTTHHLFQP LLYQVATGII SEGEIAPATR VILRKQKNAQ VLLGDVTHI DLENKTVDSV LLGHTYSTPY DSLIIAAGAG QSYFGNDHFA EFAPGMKSID DALELRGRIL GAFEQAERSS D PVRRAKLL ...String:
MSHPGATASD RHKVVIIGSG FGGLTAAKTL KRADVDVKLI ARTTHHLFQP LLYQVATGII SEGEIAPATR VILRKQKNAQ VLLGDVTHI DLENKTVDSV LLGHTYSTPY DSLIIAAGAG QSYFGNDHFA EFAPGMKSID DALELRGRIL GAFEQAERSS D PVRRAKLL TFTVVGAGPT GVEMAGQIAE LADQTLRGSF RHIDPTEARV ILLDAAPAVL PPMGEKLGKK ARARLEKMGV EV QLGAMVT DVDRNGITVK DSDGTIRRIE SACKVWSAGV SASPLGKDLA EQSGVELDRA GRVKVQPDLT LPGHPNVFVV GDM AAVEGV PGVAQGAIQG GRYAAKIIKR EVSGTSPKIR TPFEYFDKGS MATVSRFSAV AKVGPVEFAG FFAWLCWLVL HLVY LVGFK TKIVTLLSWG VTFLSTKRGQ LTITEQQAYA RTRIEELEEI AAAVQDTEKA ASFVWSTTAV SVVRIIDYKD HDGDY KDHD IDYKDDDDK

UniProtKB: NADH:ubiquinone reductase (non-electrogenic)

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #3: (3S,4R,7aR,9S,11aR)-9-(bis{[4-(trifluoromethyl)phenyl]methyl}amin...

MacromoleculeName: (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
type: ligand / ID: 3 / Number of copies: 2 / Formula: A1DCJ
Molecular weightTheoretical: 568.594 Da

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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

BufferpH: 6.8
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 286 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (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: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. v5.0.0-beta) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial model was generated ab initio in cryoSPARC v5.0.0-beta
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v5.0.0-beta) / Number images used: 62351
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v5.0.0-beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v5.0.0-beta)
FSC plot (resolution estimation)

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