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- EMDB-44775: Tethered respiratory III2IV2 supercomplex from Saccharomyces cere... -

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Basic information

Entry
Database: EMDB / ID: EMD-44775
TitleTethered respiratory III2IV2 supercomplex from Saccharomyces cerevisiae, CIVb local refinement
Map dataTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement
Sample
  • Complex: Tethered supercomplex
    • Complex: Ubiquinol-cytochrome c oxidoreductase
    • Complex: Cytochrome c oxidase
KeywordsComplex / Oxidoreductase / Respiration / ELECTRON TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsEldeeb MH / Carlstrom A / Berndtsson J / Ott M / Fontanesi F
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W911NF-21-1-0359 United States
CitationJournal: To Be Published
Title: Differential substrate utilization by yeast respiratory supercomplexes
Authors: Eldeeb MH / Cosner Z / Mays J / Carlstrom A / Rodriguez G / Berndtsson J / Ott M / Fontanesi F
History
DepositionMay 7, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44775.png

Downloads & links

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Map

FileDownload / File: emd_44775.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 450 pix.
= 508.05 Å		1.13 Å/pix.
x 450 pix.
= 508.05 Å		1.13 Å/pix.
x 450 pix.
= 508.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.129 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.8561381 - 2.8251507
Average (Standard dev.)-0.0012949379 (±0.07304206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 508.05 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44775_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Tethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local...

Fileemd_44775_half_map_1.map
AnnotationTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Tethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local...

Fileemd_44775_half_map_2.map
AnnotationTethered respiratory supercomplex from Saccharomyces cerevisiae, CIVb local refinement half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tethered supercomplex

EntireName: Tethered supercomplex
Components
  • Complex: Tethered supercomplex
    • Complex: Ubiquinol-cytochrome c oxidoreductase
    • Complex: Cytochrome c oxidase

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Supramolecule #1: Tethered supercomplex

SupramoleculeName: Tethered supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

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Supramolecule #2: Ubiquinol-cytochrome c oxidoreductase

SupramoleculeName: Ubiquinol-cytochrome c oxidoreductase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

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Supramolecule #3: Cytochrome c oxidase

SupramoleculeName: Cytochrome c oxidase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #11-#21
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303

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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

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
10.0 mMC4H11NO3Tris-HCl pH 7.5
150.0 mMNaClSodium chloride
1.0 mMC7H7FO2SPhenylmethylsulfonyl fluoride (PMSF)
1.0 mMC10H16N2O8Ethylenediaminetetraacetic acid (EDTA)
0.1 %C56H92O29Digitonin
150.0 ng/uLC120H169N31O49S3X FLAG peptide
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
Details: The grid was covered in a 3 nm ultrathin carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Details: 3 uL of sample, 5 s blot time, 30 s hold time, 0 blot force..

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12211 / Average exposure time: 2.6 sec. / Average electron dose: 55.452 e/Å2
Details: Images were collected as movies composed of 40 frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1646359
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Details: Initial model for refinement was generated ab-initio in cryoSPARC.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 47746
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2) / Details: Local refinement after particle subtraction
Final 3D classificationNumber classes: 5 / Avg.num./class: 9785 / Software - Name: cryoSPARC (ver. 4.2)
Details: Classification was performed in 3D to remove junk particles from the dataset. The final round of classification used 48,925 particles, with 48,218 ultimately being used for refinement of the predominant class.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ymx


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL

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