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- EMDB-19965: Local refinement of CIII2 from Saccharomyces cerevisiae -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-19965
TitleLocal refinement of CIII2 from Saccharomyces cerevisiae
Map data
Sample
  • Complex: III2-IV respiratory supercomplex
KeywordsRespiration / supercomplex / MEMBRANE PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWu F / Di Trani JM / Rubinstein JL / Brzezinski P / Moe A
Funding support Sweden, Canada, 3 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
Swedish Research Council Sweden
Canadian Institutes of Health Research (CIHR)PJT191893 Canada
CitationJournal: Nat Commun / Year: 2024
Title: Electron transfer in the respiratory chain at low salinity.
Authors: Ana Paula Lobez / Fei Wu / Justin M Di Trani / John L Rubinstein / Mikael Oliveberg / Peter Brzezinski / Agnes Moe /
Abstract: Recent studies have established that cellular electrostatic interactions are more influential than assumed previously. Here, we use cryo-EM and perform steady-state kinetic studies to investigate ...Recent studies have established that cellular electrostatic interactions are more influential than assumed previously. Here, we use cryo-EM and perform steady-state kinetic studies to investigate electrostatic interactions between cytochrome (cyt.) c and the complex (C) III-IV supercomplex from Saccharomyces cerevisiae at low salinity. The kinetic studies show a sharp transition with a Hill coefficient ≥2, which together with the cryo-EM data at 2.4 Å resolution indicate multiple cyt. c molecules bound along the supercomplex surface. Negatively charged loops of CIII subunits Qcr6 and Qcr9 become structured to interact with cyt. c. In addition, the higher resolution allows us to identify water molecules in proton pathways of CIV and, to the best of our knowledge, previously unresolved cardiolipin molecules. In conclusion, the lowered electrostatic screening renders engagement of multiple cyt. c molecules that are directed by electrostatically structured CIII loops to conduct electron transfer between CIII and CIV.
History
DepositionMar 27, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19965.png

Downloads & links

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Map

FileDownload / File: emd_19965.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 432 pix.
= 365.645 Å		0.85 Å/pix.
x 432 pix.
= 365.645 Å		0.85 Å/pix.
x 432 pix.
= 365.645 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.5631688 - 5.911624
Average (Standard dev.)0.0039275833 (±0.12508017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 365.6448 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3DVA class 1, Qcr9 extension to cyt. c on CIV

Fileemd_19965_additional_1.map
Annotation3DVA class 1, Qcr9 extension to cyt. c on CIV
Projections & Slices
AxesZYX

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Additional map: 3DVA class 2

Fileemd_19965_additional_2.map
Annotation3DVA class 2
Projections & Slices
AxesZYX

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Additional map: 3DVA class 3, Qcr6 extension to cyt. c on CIII

Fileemd_19965_additional_3.map
Annotation3DVA class 3, Qcr6 extension to cyt. c on CIII
Projections & Slices
AxesZYX

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Half map: Half map A

Fileemd_19965_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_19965_half_map_2.map
AnnotationHalf map B
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AxesZYX

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Sample components

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Entire : III2-IV respiratory supercomplex

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

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Supramolecule #1: III2-IV respiratory supercomplex

SupramoleculeName: III2-IV respiratory supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
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 / 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: 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: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hu9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 196457
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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