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- EMDB-50215: Subtomogram average of the Chlamydomonas reinhardtii mitochondria... -

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Basic information

Entry
Database: EMDB / ID: EMD-50215
TitleSubtomogram average of the Chlamydomonas reinhardtii mitochondrial respirasome - C2 expanded, complex III focus
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
Keywordsrespirasome / alga / respiration / mitochondria / MEMBRANE PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 6.2 Å
AuthorsWaltz F / Righetto R / Kotecha A / Engel BD
Funding support Germany, Switzerland, 2 items
OrganizationGrant numberCountry
Alexander von Humboldt Foundation Germany
Swiss National Science Foundation210561 Switzerland
CitationJournal: Science / Year: 2025
Title: In-cell architecture of the mitochondrial respiratory chain.
Authors: Florent Waltz / Ricardo D Righetto / Lorenz Lamm / Thalia Salinas-Giegé / Ron Kelley / Xianjun Zhang / Martin Obr / Sagar Khavnekar / Abhay Kotecha / Benjamin D Engel /
Abstract: Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, ...Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome . Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria.
History
DepositionApr 30, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50215.png

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Map

FileDownload / File: emd_50215.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.91 Å/pix.
x 288 pix.
= 550.08 Å		1.91 Å/pix.
x 288 pix.
= 550.08 Å		1.91 Å/pix.
x 288 pix.
= 550.08 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.91 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.48472565 - 0.881582
Average (Standard dev.)0.0004150507 (±0.012039448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 550.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50215_msk_1.map
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Half map: #1

Fileemd_50215_half_map_1.map
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Half map: #2

Fileemd_50215_half_map_2.map
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Sample components

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Entire : Chlamydomonas reinhardtii

EntireName: Chlamydomonas reinhardtii (plant)
Components
  • Cell: Chlamydomonas reinhardtii

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Supramolecule #1: Chlamydomonas reinhardtii

SupramoleculeName: Chlamydomonas reinhardtii / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 mat3-4 mt+

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
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) / Resolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 27465
ExtractionNumber tomograms: 131 / Number images used: 26591 / Method: Template Matching / Software: (Name: STOPGAP (ver. 0.7.1), PyTom (ver. 0.5.0))
Final 3D classificationSoftware - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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