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- EMDB-52267: Sub-tomogram average of the wild-type C. elegans ATP synthase dim... -

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Basic information

Entry
Database: EMDB / ID: EMD-52267
TitleSub-tomogram average of the wild-type C. elegans ATP synthase dimer (intermediate membrane curvature)
Map data
Sample
  • Organelle or cellular component: Cristae membranes isolated from wild-type C. elegans
KeywordsSupercomplex / Dimer / Enzyme / Respiration / MEMBRANE PROTEIN
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsubtomogram averaging / cryo EM / Resolution: 28.0 Å
AuthorsBuzzard E / Gold VAM / McLaren M / Zhang D
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/1 United Kingdom
CitationJournal: To Be Published
Title: The effect of NDUF-11 knockdown on respiratory chain organisation in C. elegans studied by cryo-electron tomography
Authors: Buzzard E / McLaren M / Knapp-Wilson A / Zhang D / White R / Daum B / Kuwabara PE / Collinson I / Gold VAM
History
DepositionDec 5, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52267.png

Downloads & links

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Map

FileDownload / File: emd_52267.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10 Å/pix.
x 96 pix.
= 960. Å		10 Å/pix.
x 96 pix.
= 960. Å		10 Å/pix.
x 96 pix.
= 960. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 10 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.492
Minimum - Maximum-0.902884 - 2.024507
Average (Standard dev.)0.0071944618 (±0.09628472)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 960.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52267_msk_1.map
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AxesZYX

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Additional map: #1

Fileemd_52267_additional_1.map
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Half map: #1

Fileemd_52267_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #2

Fileemd_52267_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cristae membranes isolated from wild-type C. elegans

EntireName: Cristae membranes isolated from wild-type C. elegans
Components
  • Organelle or cellular component: Cristae membranes isolated from wild-type C. elegans

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Supramolecule #1: Cristae membranes isolated from wild-type C. elegans

SupramoleculeName: Cristae membranes isolated from wild-type C. elegans / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / Strain: N2 (Bristol) / Organ: Whole organism / Tissue: Whole organism / Organelle: Mitochondria

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

Concentration10 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
220.0 mMC6H14O6Mannitol
70.0 mMC12H22O11Sucrose
5.0 mMC4H11NO3Tris-HCL
1.0 mMC14H24N2O10EGTA

Details: Basic STEG/M buffer.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMitochondria isolated from C. elegans underwent freeze-thaw, to break open the outer mitochondrial membrane and thus facilitate dispersion of cristae membranes from the dense mitochondrial matrix.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1 / Average exposure time: 1.41 sec. / Average electron dose: 1.31 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 42000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 2220
ExtractionNumber tomograms: 100 / Number images used: 7347
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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