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- EMDB-23419: Cytochrome c bound to CIV in yeast III-IV supercomplex. Local non... -

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Basic information

Entry
Database: EMDB / ID: EMD-23419
TitleCytochrome c bound to CIV in yeast III-IV supercomplex. Local non-uniform refinement of CIV-cytochrome c portion, locally filtered.
Map dataCytochrome c bound to CIV in yeast III-IV supercomplex. Local non-uniform refinement of CIV-cytochrome c portion, locally filtered.
Sample
  • Complex: yeast III-IV supercomplex with cytochrome c
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsMoe A / Di Trani J / Rubinstein J / Brzezinski P
Funding support Canada, Sweden, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Knut and Alice Wallenberg Foundation2019.0043 Sweden
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Cryo-EM structure and kinetics reveal electron transfer by 2D diffusion of cytochrome in the yeast III-IV respiratory supercomplex.
Authors: Agnes Moe / Justin Di Trani / John L Rubinstein / Peter Brzezinski /
Abstract: Energy conversion in aerobic organisms involves an electron current from low-potential donors, such as NADH and succinate, to dioxygen through the membrane-bound respiratory chain. Electron transfer ...Energy conversion in aerobic organisms involves an electron current from low-potential donors, such as NADH and succinate, to dioxygen through the membrane-bound respiratory chain. Electron transfer is coupled to transmembrane proton transport, which maintains the electrochemical proton gradient used to produce ATP and drive other cellular processes. Electrons are transferred from respiratory complexes III to IV (CIII and CIV) by water-soluble cytochrome (cyt.) In and some other organisms, these complexes assemble into larger CIIICIV supercomplexes, the functional significance of which has remained enigmatic. In this work, we measured the kinetics of the supercomplex cyt. -mediated QH:O oxidoreductase activity under various conditions. The data indicate that the electronic link between CIII and CIV is confined to the surface of the supercomplex. Single-particle electron cryomicroscopy (cryo-EM) structures of the supercomplex with cyt. show the positively charged cyt. bound to either CIII or CIV or along a continuum of intermediate positions. Collectively, the structural and kinetic data indicate that cyt. travels along a negatively charged patch on the supercomplex surface. Thus, rather than enhancing electron transfer rates by decreasing the distance that cyt. must diffuse in three dimensions, formation of the CIIICIV supercomplex facilitates electron transfer by two-dimensional (2D) diffusion of cyt. This mechanism enables the CIIICIV supercomplex to increase QH:O oxidoreductase activity and suggests a possible regulatory role for supercomplex formation in the respiratory chain.
History
DepositionFeb 4, 2021-
Header (metadata) releaseApr 21, 2021-
Map releaseApr 21, 2021-
UpdateApr 21, 2021-
Current statusApr 21, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.325
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.325
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23419.png

Downloads & links

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Map

FileDownload / File: emd_23419.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytochrome c bound to CIV in yeast III-IV supercomplex. Local non-uniform refinement of CIV-cytochrome c portion, locally filtered.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 380 pix.
= 391.4 Å		1.03 Å/pix.
x 380 pix.
= 391.4 Å		1.03 Å/pix.
x 380 pix.
= 391.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.325 / Movie #1: 0.325
Minimum - Maximum-0.36772296 - 1.5731809
Average (Standard dev.)0.0018656043 (±0.030283371)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 391.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z391.400391.400391.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.3681.5730.002

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Supplemental data

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Sample components

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Entire : yeast III-IV supercomplex with cytochrome c

EntireName: yeast III-IV supercomplex with cytochrome c
Components
  • Complex: yeast III-IV supercomplex with cytochrome c

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Supramolecule #1: yeast III-IV supercomplex with cytochrome c

SupramoleculeName: yeast III-IV supercomplex with cytochrome c / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's 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: 7.4
VitrificationCryogen name: ETHANE-PROPANE
Detailsmonodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 24362
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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