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- EMDB-0006: Saccharomyces cerevisiae supercomplex class2 (III2IV2) -

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Basic information

Entry
Database: EMDB / ID: EMD-0006
TitleSaccharomyces cerevisiae supercomplex class2 (III2IV2)
Map data
SampleSaccharomyces cerevisiae Supercomplex
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0006.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.22 / Movie #1: 0.28
Minimum - Maximum-0.5725007 - 1.5357721
Average (Standard dev.)0.0071697747 (±0.061136417)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z392.200392.200392.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-0.5731.5360.007

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Supplemental data

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Half map: Halfmap1 Class2

Fileemd_0006_half_map_1.map
AnnotationHalfmap1 Class2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Halfmap2 Class2

Fileemd_0006_half_map_2.map
AnnotationHalfmap2 Class2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Saccharomyces cerevisiae Supercomplex

EntireName: Saccharomyces cerevisiae Supercomplex / Number of components: 1

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Component #1: protein, Saccharomyces cerevisiae Supercomplex

ProteinName: Saccharomyces cerevisiae Supercomplex / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae W303 (yeast)
Source (natural)Organelle: Mitochondria

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 108043
3D reconstructionSoftware: cryoSPARC / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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