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- EMDB-18063: Local refinement of CIII2 from S. pombe -

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Basic information

Entry
Database: EMDB / ID: EMD-18063
TitleLocal refinement of CIII2 from S. pombe
Map data
Sample
  • Complex: III2-IV1 respiratory supercomplex
KeywordsSupercomplex / respiration / MEMBRANE PROTEIN
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsMoe A / Brzezinski P
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure and function of the III-IV-cyt supercomplex.
Authors: Agnes Moe / Anna-Roza Dimogkioka / Doron Rapaport / Linda Näsvik Öjemyr / Peter Brzezinski /
Abstract: The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the ...The respiratory chain in aerobic organisms is composed of a number of membrane-bound protein complexes that link electron transfer to proton translocation across the membrane. In mitochondria, the final electron acceptor, complex IV (CIV), receives electrons from dimeric complex III (CIII), via a mobile electron carrier, cytochrome . In the present study, we isolated the CIIICIV supercomplex from the fission yeast and determined its structure with bound cyt. using single-particle electron cryomicroscopy. A respiratory supercomplex factor 2 was found to be bound at CIV distally positioned in the supercomplex. In addition to the redox-active metal sites, we found a metal ion, presumably Zn, coordinated in the CIII subunit Cor1, which is encoded by the same gene () as the mitochondrial-processing peptidase subunit β. Our data show that the isolated CIIICIV supercomplex displays proteolytic activity suggesting a dual role of CIII in . As in the supercomplex from , subunit Cox5 of CIV faces towards one CIII monomer, but in the two complexes are rotated relative to each other by ~45°. This orientation yields equal distances between the cyt. binding sites at CIV and at each of the two CIII monomers. The structure shows cyt. bound at four positions, but only along one of the two symmetrical branches. Overall, this combined structural and functional study reveals the integration of peptidase activity with the CIII respiratory system and indicates a two-dimensional cyt. diffusion mechanism within the CIII-CIV supercomplex.
History
DepositionJul 31, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18063.png

Downloads & links

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Map

FileDownload / File: emd_18063.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 512 pix.
= 433.357 Å		0.85 Å/pix.
x 512 pix.
= 433.357 Å		0.85 Å/pix.
x 512 pix.
= 433.357 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4026961 - 0.835254
Average (Standard dev.)0.0008807975 (±0.024861073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 433.3568 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18063_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_18063_half_map_2.map
Projections & Slices
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Sample components

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Entire : III2-IV1 respiratory supercomplex

EntireName: III2-IV1 respiratory supercomplex
Components
  • Complex: III2-IV1 respiratory supercomplex

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Supramolecule #1: III2-IV1 respiratory supercomplex

SupramoleculeName: III2-IV1 respiratory supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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) / Average electron dose: 41.0 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: 0.6 µm / Nominal magnification: 105000
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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 125752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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