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- EMDB-40645: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Loc... -

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Basic information

Entry
Database: EMDB / ID: EMD-40645
Titlecytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform)
Map datacytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform, locally sharpened)
Sample
  • Complex: cytochrome bc1-cbb3 supercomplex
KeywordsElectron transport chain / Supercomplex / Pseudomonas aeruginosa / MEMBRANE PROTEIN
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDi Trani JM / Rubinstein JL
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canadian Institutes of Health Research (CIHR)PJT451412 Canada
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure of the - respiratory supercomplex from .
Authors: Justin M Di Trani / Andreea A Gheorghita / Madison Turner / Peter Brzezinski / Pia Ädelroth / Siavash Vahidi / P Lynne Howell / John L Rubinstein /
Abstract: Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that ...Energy conversion by electron transport chains occurs through the sequential transfer of electrons between protein complexes and intermediate electron carriers, creating the proton motive force that enables ATP synthesis and membrane transport. These protein complexes can also form higher order assemblies known as respiratory supercomplexes (SCs). The electron transport chain of the opportunistic pathogen is closely linked with its ability to invade host tissue, tolerate harsh conditions, and resist antibiotics but is poorly characterized. Here, we determine the structure of a SC that forms between the quinol:cytochrome oxidoreductase (cytochrome ) and one of the organism's terminal oxidases, cytochrome , which is found only in some bacteria. Remarkably, the SC structure also includes two intermediate electron carriers: a diheme cytochrome and a single heme cytochrome . Together, these proteins allow electron transfer from ubiquinol in cytochrome to oxygen in cytochrome . We also present evidence that different isoforms of cytochrome can participate in formation of this SC without changing the overall SC architecture. Incorporating these different subunit isoforms into the SC would allow the bacterium to adapt to different environmental conditions. Bioinformatic analysis focusing on structural motifs in the SC suggests that cytochrome - SCs also exist in other bacterial pathogens.
History
DepositionApr 28, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40645.png

Downloads & links

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Map

FileDownload / File: emd_40645.map.gz / Format: CCP4 / Size: 139.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform, locally sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 332 pix.
= 341.96 Å		1.03 Å/pix.
x 332 pix.
= 341.96 Å		1.03 Å/pix.
x 332 pix.
= 341.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.65
Minimum - Maximum-0.24146175 - 14.073979
Average (Standard dev.)0.0025555629 (±0.14680709)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions332332332
Spacing332332332
CellA=B=C: 341.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40645_additional_1.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform, unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40645_half_map_1.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform, half map A)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined...

Fileemd_40645_half_map_2.map
Annotationcytochrome bc1-cbb3 supercomplex from Pseudomonas aeruginosa (Locally refined cytochrome cbb3 with CcoP2 isoform, half map 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 : cytochrome bc1-cbb3 supercomplex

EntireName: cytochrome bc1-cbb3 supercomplex
Components
  • Complex: cytochrome bc1-cbb3 supercomplex

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Supramolecule #1: cytochrome bc1-cbb3 supercomplex

SupramoleculeName: cytochrome bc1-cbb3 supercomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 374 kDa/nm

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.0 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: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 24187
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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