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- EMDB-0005: Saccharomyces cerevisiae supercomplex class 1 (III2IV) -

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Basic information

Entry
Database: EMDB / ID: EMD-0005
TitleSaccharomyces cerevisiae supercomplex class 1 (III2IV)
Map dataSaccharomyces cerevisiae Class1 (III2IV)
Sample
  • Complex: Saccharomyces cerevisiae Supercomplex (III2IV)
    • Complex: Saccharomyces cerevisiae complex III
    • Complex: Saccharomyces cerevisiae complex IV
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsRathore S / Berndtsson J / Conrad J / Ott M
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Cryo-EM structure of the yeast respiratory supercomplex.
Authors: Sorbhi Rathore / Jens Berndtsson / Lorena Marin-Buera / Julian Conrad / Marta Carroni / Peter Brzezinski / Martin Ott /
Abstract: Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes ...Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes IIIIV and IIIIV, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.
History
DepositionMay 15, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseJan 2, 2019-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: PDBe / Status: Released

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Structure visualization

Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0005.png

Downloads & links

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Map

FileDownload / File: emd_0005.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSaccharomyces cerevisiae Class1 (III2IV)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 370 pix.
= 392.2 Å		1.06 Å/pix.
x 370 pix.
= 392.2 Å		1.06 Å/pix.
x 370 pix.
= 392.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-1.0410119 - 2.3215709
Average (Standard dev.)0.008701679 (±0.07678789)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 392.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Halfmap1 class1

Fileemd_0005_half_map_1.map
AnnotationHalfmap1 class1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap2 class1

Fileemd_0005_half_map_2.map
AnnotationHalfmap2 class1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Saccharomyces cerevisiae Supercomplex (III2IV)

EntireName: Saccharomyces cerevisiae Supercomplex (III2IV)
Components
  • Complex: Saccharomyces cerevisiae Supercomplex (III2IV)
    • Complex: Saccharomyces cerevisiae complex III
    • Complex: Saccharomyces cerevisiae complex IV

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Supramolecule #1: Saccharomyces cerevisiae Supercomplex (III2IV)

SupramoleculeName: Saccharomyces cerevisiae Supercomplex (III2IV) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria

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Supramolecule #2: Saccharomyces cerevisiae complex III

SupramoleculeName: Saccharomyces cerevisiae complex III / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#13
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria

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Supramolecule #3: Saccharomyces cerevisiae complex IV

SupramoleculeName: Saccharomyces cerevisiae complex IV / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #14-#25
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Organelle: Mitochondria

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: ABINITIO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 107845
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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