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- EMDB-47124: Cryo-EM structure of Mycobacterium smegmatis ATP synthase rotatio... -

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Entry
Database: EMDB / ID: EMD-47124
TitleCryo-EM structure of Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles
Map dataCryo-EM structure of Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles (sharpened)
Sample
  • Complex: Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles
KeywordsATP synthase Inverted membrane vesicles / TRANSLOCASE
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsCourbon GM / Rubinstein JL
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM of native membranes reveals an intimate connection between the Krebs cycle and aerobic respiration in mycobacteria.
Authors: Justin M Di Trani / Jiacheng Yu / Gautier M Courbon / Ana Paula Lobez Rodriguez / Chen-Yi Cheung / Yingke Liang / Claire E Coupland / Stephanie A Bueler / Gregory M Cook / Peter Brzezinski / ...Authors: Justin M Di Trani / Jiacheng Yu / Gautier M Courbon / Ana Paula Lobez Rodriguez / Chen-Yi Cheung / Yingke Liang / Claire E Coupland / Stephanie A Bueler / Gregory M Cook / Peter Brzezinski / John L Rubinstein /
Abstract: To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from , enriched for vesicles containing complexes of interest, and imaged ...To investigate the structure of the mycobacterial oxidative phosphorylation machinery, we prepared inverted membrane vesicles from , enriched for vesicles containing complexes of interest, and imaged the vesicles with electron cryomicroscopy. We show that this analysis allows determination of the structure of both mycobacterial ATP synthase and the supercomplex of respiratory complexes III and IV in their native membrane. The latter structure reveals that the enzyme malate:quinone oxidoreductase (Mqo) physically associates with the respiratory supercomplex, an interaction that is lost on extraction of the proteins from the lipid bilayer. Mqo catalyzes an essential reaction in the Krebs cycle, and in vivo survival of mycobacterial pathogens is compromised when its activity is absent. We show with high-speed spectroscopy that the Mqo:supercomplex interaction enables rapid electron transfer from malate to the supercomplex. Further, the respiratory supercomplex is necessary for malate-driven, but not NADH-driven, electron transport chain activity and oxygen consumption. Together, these findings indicate a connection between the Krebs cycle and aerobic respiration that directs electrons along a single branch of the mycobacterial electron transport chain.
History
DepositionSep 25, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47124.png

Downloads & links

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Map

FileDownload / File: emd_47124.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 220 pix.
= 395.516 Å		1.8 Å/pix.
x 220 pix.
= 395.516 Å		1.8 Å/pix.
x 220 pix.
= 395.516 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7978 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.40963003 - 0.67169636
Average (Standard dev.)0.00029036924 (±0.04070796)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 395.516 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of Mycobacterium smegmatis ATP synthase rotational...

Fileemd_47124_additional_1.map
AnnotationCryo-EM structure of Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of Mycobacterium smegmatis ATP synthase rotational...

Fileemd_47124_half_map_1.map
AnnotationCryo-EM structure of Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles (Half A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of Mycobacterium smegmatis ATP synthase rotational...

Fileemd_47124_half_map_2.map
AnnotationCryo-EM structure of Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles (Half B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium smegmatis ATP synthase rotational state 1 in invert...

EntireName: Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles
Components
  • Complex: Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles

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Supramolecule #1: Mycobacterium smegmatis ATP synthase rotational state 1 in invert...

SupramoleculeName: Mycobacterium smegmatis ATP synthase rotational state 1 in inverted membrane vesicles
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3148
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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