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- EMDB-18991: Sub-tomogram average of the C. elegans ATP synthase dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-18991
TitleSub-tomogram average of the C. elegans ATP synthase dimer
Map dataPost-processed sub-tomogram averaging map of the C. elegans ATP synthase dimer at a nominal resolution of 38.6 Angstrom.
Sample
  • Complex: C. elegans mitochondrial ATP synthase dimer
KeywordsSupercomplex / dimer / enzyme / respiration. / MEMBRANE PROTEIN
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsubtomogram averaging / cryo EM / Resolution: 38.6 Å
AuthorsBuzzard EJ / McLaren M / Gold VAM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T008741/1 United Kingdom
CitationJournal: Biochem J / Year: 2024
Title: The consequence of ATP synthase dimer angle on mitochondrial morphology studied by cryo-electron tomography.
Authors: Emma Buzzard / Mathew McLaren / Piotr Bragoszewski / Andrea Brancaccio / Holly Ford / Bertram Daum / Patricia Kuwabara / Ian Collinson / Vicki Gold /
Abstract: Mitochondrial ATP synthases form rows of dimers, which induce membrane curvature to give cristae their characteristic lamellar or tubular morphology. The angle formed between the central stalks of ...Mitochondrial ATP synthases form rows of dimers, which induce membrane curvature to give cristae their characteristic lamellar or tubular morphology. The angle formed between the central stalks of ATP synthase dimers varies between species. Using cryo-electron tomography and sub-tomogram averaging, we determined the structure of the ATP synthase dimer from the nematode worm C. elegans and show that the dimer angle differs from previously determined structures. The consequences of this species-specific difference at the dimer interface were investigated by comparing C. elegans and S. cerevisiae mitochondrial morphology. We reveal that C. elegans has a larger ATP synthase dimer angle with more lamellar (flatter) cristae when compared to yeast. The underlying cause of this difference was investigated by generating an atomic model of the C. elegans ATP synthase dimer by homology modelling. A comparison of our C. elegans model to an existing S. cerevisiae structure reveals the presence of extensions and rearrangements in C. elegans subunits associated with maintaining the dimer interface. We speculate that increasing dimer angles could provide an advantage for species that inhabit variable-oxygen environments by forming flatter more energetically efficient cristae.
History
DepositionNov 27, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18991.png

Downloads & links

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Map

FileDownload / File: emd_18991.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed sub-tomogram averaging map of the C. elegans ATP synthase dimer at a nominal resolution of 38.6 Angstrom.
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.58 Å/pix.
x 140 pix.
= 501.2 Å		3.58 Å/pix.
x 140 pix.
= 501.2 Å		3.58 Å/pix.
x 140 pix.
= 501.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.58 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0429
Minimum - Maximum-0.12787773 - 0.2490444
Average (Standard dev.)0.0040603867 (±0.027478052)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 501.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18991_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: Half map 1 from relion refinement job used...

Fileemd_18991_half_map_1.map
AnnotationHalf map 1 from relion refinement job used to generate final post-processed map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from relion refinement job used...

Fileemd_18991_half_map_2.map
AnnotationHalf map 2 from relion refinement job used to generate final post-processed 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 : C. elegans mitochondrial ATP synthase dimer

EntireName: C. elegans mitochondrial ATP synthase dimer
Components
  • Complex: C. elegans mitochondrial ATP synthase dimer

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Supramolecule #1: C. elegans mitochondrial ATP synthase dimer

SupramoleculeName: C. elegans mitochondrial ATP synthase dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Caenorhabditis elegans (invertebrata) / Strain: N2 (Bristol) / Organ: Whole organism / Tissue: Whole organism / Organelle: Mitochondria / Location in cell: Inner mitochondrial membrane

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
220.0 mMC6H14O6Mannitol
70.0 mMC12H22O11Sucrose
5.0 mMC4H11NO3Tris-HCLTris
1.0 mMC14H24N2O10EGTA
GridModel: UltrAuFoil 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsMitochondria isolated from C. elegans underwent 2-3 freeze-thaw cycles, to break open the mitochondria and release the cristae. Tomography was completed using these crista membranes.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 7.0 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 39000
Specialist opticsEnergy filter - Name: GIF Quantum LS
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 3 / Average exposure time: 2.8 sec. / Average electron dose: 1.36 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 50 / Number images used: 3234
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 38.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 1755
FSC plot (resolution estimation)

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