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- EMDB-70545: Structure of Mycobacterium smegmatis EtfD -

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Basic information

Entry
Database: EMDB / ID: EMD-70545
TitleStructure of Mycobacterium smegmatis EtfD
Map dataCryoEM map of Mycobacterium smegmatis EtfD (sharpened)
Sample
  • Complex: Structure of Mycobacterium smegmatis EtfD
    • Protein or peptide: Iron-sulfur-binding reductase
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: MENAQUINONE-9
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane
Keywordsoxidoreductase / membrane protein / electron transport chain / beta oxidation
Function / homology
Function and homology information


4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / plasma membrane
Similarity search - Function
4Fe-4S dicluster domain / : / Cysteine-rich domain / Cysteine-rich domain / Alpha-helical ferredoxin / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Iron-sulfur-binding reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsCourbon GM / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: EMBO J / Year: 2026
Title: Structural basis for EtfD-mediated coupling of β-oxidation and the respiratory chain in mycobacteria.
Authors: Gautier M Courbon / Vadim Makarov / Stewart T Cole / Dirk Schnapinger / Sabine Ehrt / John L Rubinstein /
Abstract: Targeting β-oxidation has been proposed as a strategy for shortening tuberculosis (TB) treatment by killing non-replicating Mycobacterium tuberculosis within granulomas where the pathogen relies on ...Targeting β-oxidation has been proposed as a strategy for shortening tuberculosis (TB) treatment by killing non-replicating Mycobacterium tuberculosis within granulomas where the pathogen relies on host-derived lipids. The protein EtfD is thought to couple β-oxidation of fatty acids with the respiratory chain in mycobacteria. However, the structure of EtfD is not known and, as the presumed link between two complex processes, its activity has been difficult to measure, impeding its exploitation as a drug target. Here we show that Mycobacterium smegmatis, a fast growing and nonpathogenic model for M. tuberculosis, relies on EtfD for extracting energy from β-oxidation. The electron cryomicroscopy structure of M. smegmatis EtfD reveals an unusual linear [3Fe-4S] cluster that has not been seen in other protein structures, and suggests how EtfD transfers electrons from β-oxidation to the respiratory chain. We devised an assay that couples EtfD activity to a fluorescent readout of proton pumping by the respiratory chain, which can be used to identify compounds that block mycobacteria from using β-oxidation to power oxidative phosphorylation.
History
DepositionMay 8, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70545.png

Downloads & links

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Map

FileDownload / File: emd_70545.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 320 pix.
= 327.68 Å		1.02 Å/pix.
x 320 pix.
= 327.68 Å		1.02 Å/pix.
x 320 pix.
= 327.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.024 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.0467362 - 1.7700719
Average (Standard dev.)-0.000009377364 (±0.019762378)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 327.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: CryoEM map of Mycobacterium smegmatis EtfD (unsharpened)

Fileemd_70545_additional_1.map
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM map of Mycobacterium smegmatis EtfD (Half B)

Fileemd_70545_half_map_1.map
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (Half B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM map of Mycobacterium smegmatis EtfD (Half A)

Fileemd_70545_half_map_2.map
AnnotationCryoEM map of Mycobacterium smegmatis EtfD (Half A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of Mycobacterium smegmatis EtfD

EntireName: Structure of Mycobacterium smegmatis EtfD
Components
  • Complex: Structure of Mycobacterium smegmatis EtfD
    • Protein or peptide: Iron-sulfur-binding reductase
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: MENAQUINONE-9
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: Non-cubane [4Fe-4S]-cluster
  • Ligand: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane

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Supramolecule #1: Structure of Mycobacterium smegmatis EtfD

SupramoleculeName: Structure of Mycobacterium smegmatis EtfD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: Iron-sulfur-binding reductase

MacromoleculeName: Iron-sulfur-binding reductase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Molecular weightTheoretical: 111.045625 KDa
SequenceString: MAHTLEVSRL IIGLLMTAIV LVFAAKRVLW LTKLIRSGQK TLDENGRKND LQKRITTQIT EVFGQTRLLR WSVPGIAHFF TMWGFFVLA SVYLEAYGVL FDPEFHIPFI GRWPVLGFLQ DFFAVAVLLG IIVFAIIRVV REPKKIGRDS RFYGSHTGGA W EILFMIFL ...String:
MAHTLEVSRL IIGLLMTAIV LVFAAKRVLW LTKLIRSGQK TLDENGRKND LQKRITTQIT EVFGQTRLLR WSVPGIAHFF TMWGFFVLA SVYLEAYGVL FDPEFHIPFI GRWPVLGFLQ DFFAVAVLLG IIVFAIIRVV REPKKIGRDS RFYGSHTGGA W EILFMIFL VIATYALFRG AAVNTLGERF PYQSGAFFSD FMAWILRPLG ATANMWIETV ALMGHIGVML VFLLIVLHSK HL HIGLAPI NVTFKRLPNG LGPLLPMESN GEYIDFEDPA EDAVFGKGKI EDFTWKGYLD FTTCTECGRC QSQCPAWNTG KPL SPKLVI MNLRDHMFAK APYILGEKPS PLESTPEGGL GEKARGEKHE QKHAHDHVPE SGFERILGSG PEQALRPLVG TEEQ GGVID PDVLWSCTNC GACVEQCPVD IEHIDHIVDM RRYQVMVESE FPGELGVLFK NLETKGNPWG QNAKDRTNWI DEVDF DVPV YGEDVDSFDG FEYLFWVGCA GAYEDRAKKT TKAVAELLAT AGVKFLVLGT GETCTGDSAR RSGNEFLFQQ LAAQNV ETI NELFEGVETV DRKIVVTCPH CFNTIGREYP QLGANYSVVH HTQLLNRLVR DKKLVPVKSV SEQNGQPVTY HDPCFLG RH NKVYEAPREL VEASGVTLKE MPRHADRGLC CGAGGARMWM EEHIGKRVNV ERTEEAMDTA STIATGCPFC RVMITDGV D DVAASRNVEK AEVLDVAQLL LNSLDTSKVT LPEKGTAAKE SEKRAAARAE AEAKAEAAAP PVEEAAPEAE APAAPAAGG AEAKPVTGLG MAGAAKRPGA KKAAPAAEAS AAPAAAPAPA KGLGLAGGAK RPGAKKAAAP AAEAPAAPAS DAPPVKGLGL AGGAKRPGA KKTAAAAPAE KPAATEAPEA SATPAAPAAP VKGLGLAAGA KRPGAKKTAA APAEKPAAAE TEAPAPAETA A PAEPAKPE PPVVGLGIAA GARRPGAKKA AAKPAAAPAP AAEKPAEQAA EPEKPAEKPA EPEKPEPPVV GLGIKPGAKR PG KR

UniProtKB: Iron-sulfur-binding reductase

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 1 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #3: MENAQUINONE-9

MacromoleculeName: MENAQUINONE-9 / type: ligand / ID: 3 / Number of copies: 1 / Formula: MQ9
Molecular weightTheoretical: 785.233 Da
Chemical component information

ChemComp-MQ9:
MENAQUINONE-9

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Macromolecule #4: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 4 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #5: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #6: Non-cubane [4Fe-4S]-cluster

MacromoleculeName: Non-cubane [4Fe-4S]-cluster / type: ligand / ID: 6 / Number of copies: 1 / Formula: 9S8
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-9S8:
Non-cubane [4Fe-4S]-cluster

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Macromolecule #7: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane

MacromoleculeName: 1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane
type: ligand / ID: 7 / Number of copies: 1 / Formula: A1CBX
Molecular weightTheoretical: 295.795 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48053
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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