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- EMDB-15335: Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide... -

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Basic information

Entry
Database: EMDB / ID: EMD-15335
TitleComplex III2 from Yarrowia lipolytica, oxidised with ferricyanide, Rieske domains in b- and c-position
Map data
Sample
  • Organelle or cellular component: Complex III2, oxidised with ferricyanide, asymmetric dimer with Rieske domains in b- and c-position
Keywordsoxidoreductase / electron transport chain / MEMBRANE PROTEIN
Biological speciesYarrowia lipolytica (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWieferig J / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Complex III2 from Yarrowia lipolytica, oxidised with ferricyanide, Rieske domains in b- and c-position
Authors: Wieferig J / Kuehlbrandt W
History
DepositionJul 5, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15335.png

Downloads & links

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Map

FileDownload / File: emd_15335.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å		0.84 Å/pix.
x 360 pix.
= 301.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0126
Minimum - Maximum-0.021790676 - 0.07547947
Average (Standard dev.)0.00017465872 (±0.0028550185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 301.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_15335_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15335_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex III2, oxidised with ferricyanide, asymmetric dimer with R...

EntireName: Complex III2, oxidised with ferricyanide, asymmetric dimer with Rieske domains in b- and c-position
Components
  • Organelle or cellular component: Complex III2, oxidised with ferricyanide, asymmetric dimer with Rieske domains in b- and c-position

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Supramolecule #1: Complex III2, oxidised with ferricyanide, asymmetric dimer with R...

SupramoleculeName: Complex III2, oxidised with ferricyanide, asymmetric dimer with Rieske domains in b- and c-position
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Yarrowia lipolytica (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
GridModel: UltrAuFoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 30714
Initial angle assignmentType: OTHER / Software - Name: RELION
Final angle assignmentType: OTHER / Software - Name: RELION
Final 3D classificationNumber classes: 4 / Software - Name: RELION
FSC plot (resolution estimation)

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