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- EMDB-18021: global refinement of C respirasome, murine liver -

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Basic information

Entry
Database: EMDB / ID: EMD-18021
Titleglobal refinement of C respirasome, murine liver
Map dataglobal refinement of C respirasome
Sample
  • Complex: C respirasome from murine liver
KeywordsRespiratory chain super complex / mammalian mitochondria / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsVercellino I / Sazanov LA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101020697European Union
Citation
Journal: Nat Struct Mol Biol / Year: 2024
Title: SCAF1 drives the compositional diversity of mammalian respirasomes.
Authors: Irene Vercellino / Leonid A Sazanov /
Abstract: Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies ...Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of 'respirasome', supercomplexes made of CI, CIII and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the 'canonical' respirasome (the C-respirasome, CICIIICIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the 'back' of CI, instead of the 'toe'. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Afonine PV / Adams PD
History
DepositionJul 25, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18021.png

Downloads & links

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Map

FileDownload / File: emd_18021.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationglobal refinement of C respirasome
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 600 pix.
= 636. Å		1.06 Å/pix.
x 600 pix.
= 636. Å		1.06 Å/pix.
x 600 pix.
= 636. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.07426976 - 0.1893525
Average (Standard dev.)0.0000069935877 (±0.005434721)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 635.99994 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18021_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18021_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : C respirasome from murine liver

EntireName: C respirasome from murine liver
Components
  • Complex: C respirasome from murine liver

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Supramolecule #1: C respirasome from murine liver

SupramoleculeName: C respirasome from murine liver / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#67
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD1 / Organ: liver / Organelle: mitochondria
Molecular weightTheoretical: 1.7 MDa

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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

Concentration0.3 mg/mL
BufferpH: 7.7
Component:
ConcentrationFormulaName
50.0 mMNaClsodium chloride
20.0 mMC8H18N2O4SHEPES
2.0 mMC10H16N2O8EDTA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9453 / Average exposure time: 4.4 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1758187
Startup modelType of model: OTHER
Details: map obtained from previous processing of test dataset
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103207
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6g2j

source_name: PDB, initial_model_type: experimental modelCI

7o3c

source_name: PDB, initial_model_type: experimental modelCIII and CIV
Detailsinitial fitting done in chimera
RefinementProtocol: RIGID BODY FIT

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