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- EMDB-50208: Structure of the Chlamydomonas reinhardtii respiratory supercompl... -

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Basic information

Entry
Database: EMDB / ID: EMD-50208
TitleStructure of the Chlamydomonas reinhardtii respiratory supercomplex, focused on complex I proximal membrane part
Map data
Sample
  • Complex: Chlamydomonas reinhardtii respirasome
KeywordsMitochondria / respiratory complex / respiration / alga / MEMBRANE PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 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_50208.png

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Map

FileDownload / File: emd_50208.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 588 pix.
= 589.6 Å		1 Å/pix.
x 588 pix.
= 589.6 Å		1 Å/pix.
x 588 pix.
= 589.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.00272 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.152
Minimum - Maximum-0.539145 - 0.98854214
Average (Standard dev.)-0.00050733215 (±0.030300664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 589.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50208_msk_1.map
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Half map: #2

Fileemd_50208_half_map_1.map
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Half map: #1

Fileemd_50208_half_map_2.map
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Sample components

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Entire : Chlamydomonas reinhardtii respirasome

EntireName: Chlamydomonas reinhardtii respirasome
Components
  • Complex: Chlamydomonas reinhardtii respirasome

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Supramolecule #1: Chlamydomonas reinhardtii respirasome

SupramoleculeName: Chlamydomonas reinhardtii respirasome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 83443
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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