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- EMDB-11604: Respiratory chain supercomplex I1III2IV2 in rat heart mitochondria -

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Basic information

Entry
Database: EMDB / ID: EMD-11604
TitleRespiratory chain supercomplex I1III2IV2 in rat heart mitochondria
Map data
Sample
  • Complex: Respiratory supercomplex I1III3IV2 from Rattus norvegicus
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 27.7 Å
AuthorsChesnokov YM / Kamyshinsky RA
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-04-00835 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2021
Title: Ordered Clusters of the Complete Oxidative Phosphorylation System in Cardiac Mitochondria.
Authors: Semen Nesterov / Yury Chesnokov / Roman Kamyshinsky / Alisa Panteleeva / Konstantin Lyamzaev / Raif Vasilov / Lev Yaguzhinsky /
Abstract: The existence of a complete oxidative phosphorylation system (OXPHOS) supercomplex including both electron transport system and ATP synthases has long been assumed based on functional evidence. ...The existence of a complete oxidative phosphorylation system (OXPHOS) supercomplex including both electron transport system and ATP synthases has long been assumed based on functional evidence. However, no structural confirmation of the docking between ATP synthase and proton pumps has been obtained. In this study, cryo-electron tomography was used to reveal the supramolecular architecture of the rat heart mitochondria cristae during ATP synthesis. Respirasome and ATP synthase structure in situ were determined using subtomogram averaging. The obtained reconstructions of the inner mitochondrial membrane demonstrated that rows of respiratory chain supercomplexes can dock with rows of ATP synthases forming oligomeric ordered clusters. These ordered clusters indicate a new type of OXPHOS structural organization. It should ensure the quickness, efficiency, and damage resistance of OXPHOS, providing a direct proton transfer from pumps to ATP synthase along the lateral pH gradient without energy dissipation.
History
DepositionAug 10, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 10, 2021-
Current statusMar 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11604.png

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Map

FileDownload / File: emd_11604.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
7.4 Å/pix.
x 60 pix.
= 444. Å		7.4 Å/pix.
x 60 pix.
= 444. Å		7.4 Å/pix.
x 60 pix.
= 444. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 7.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-5.4291697 - 10.787564
Average (Standard dev.)0.025291236 (±1.4403093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.47.47.4
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z444.000444.000444.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-5.42910.7880.025

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Supplemental data

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Mask #1

Fileemd_11604_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_11604_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11604_half_map_2.map
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Sample components

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Entire : Respiratory supercomplex I1III3IV2 from Rattus norvegicus

EntireName: Respiratory supercomplex I1III3IV2 from Rattus norvegicus
Components
  • Complex: Respiratory supercomplex I1III3IV2 from Rattus norvegicus

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Supramolecule #1: Respiratory supercomplex I1III3IV2 from Rattus norvegicus

SupramoleculeName: Respiratory supercomplex I1III3IV2 from Rattus norvegicus
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: Wistar rats / Organ: heart / Organelle: Mitochondrion
Molecular weightTheoretical: 1.88 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2.5 seconds.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Cs image corrector (CEOS, Germany)
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average exposure time: 1.5 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 8.0 µm / Calibrated defocus min: 6.0 µm / Calibrated magnification: 37837 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 18000
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

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 27.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number subtomograms used: 944
ExtractionNumber tomograms: 2 / Number images used: 1706 / Software - Name: RELION (ver. 2.1) / Software - details: extraction
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Details: 3D models for the contrast transfer function (CTF) in RELION
Final 3D classificationNumber classes: 2 / Avg.num./class: 944 / Software - Name: RELION (ver. 2.1)
Details: Focused 3D classification was performed using mask on the IVb complex.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

5xtd

,

1bgy

,

5z62

)
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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