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- EMDB-50000: In situ structure of mitochondrial ATPsynthase in whole Polytomel... -

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Basic information

Entry
Database: EMDB / ID: EMD-50000
TitleIn situ structure of mitochondrial ATPsynthase in whole Polytomella cells
Map dataPrimary map of the consensus dimer used for symmetry expansion
Sample
  • Cell: Polytomella sp.
KeywordsATP synthesis / in situ / OXPHOS / MEMBRANE PROTEIN
Biological speciesPolytomella (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 6.8 Å
AuthorsDietrich L / Kuehlbrandt W / Agip ANA
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)FOR2848 Germany
CitationJournal: Science / Year: 2024
Title: In situ structure and rotary states of mitochondrial ATP synthase in whole cells.
Authors: Lea Dietrich / Ahmed-Noor A Agip / Christina Kunz / Andre Schwarz / Werner Kühlbrandt /
Abstract: Cells depend on a continuous supply of adenosine triphosphate (ATP), the universal energy currency. In mitochondria, ATP is produced by a series of redox reactions, whereby an electrochemical ...Cells depend on a continuous supply of adenosine triphosphate (ATP), the universal energy currency. In mitochondria, ATP is produced by a series of redox reactions, whereby an electrochemical gradient is established across the inner mitochondrial membrane. The ATP synthase harnesses the energy of the gradient to generate ATP from adenosine diphosphate (ADP) and inorganic phosphate. We determined the structure of ATP synthase within mitochondria of the unicellular flagellate by electron cryo-tomography and subtomogram averaging at up to 4.2-angstrom resolution, revealing six rotary positions of the central stalk, subclassified into 21 substates of the F head. The ATP synthase forms helical arrays with multiple adjacent rows defining the cristae ridges. The structure of ATP synthase under native operating conditions in the presence of a membrane potential represents a pivotal step toward the analysis of membrane protein complexes in situ.
History
DepositionMar 29, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50000.png

Downloads & links

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Map

FileDownload / File: emd_50000.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map of the consensus dimer used for symmetry expansion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.39 Å/pix.
x 140 pix.
= 475.16 Å		3.39 Å/pix.
x 140 pix.
= 475.16 Å		3.39 Å/pix.
x 140 pix.
= 475.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.394 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.25936225 - 0.8784002
Average (Standard dev.)0.023186598 (±0.12574376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 475.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Second half map of the consensus dimer at...

Fileemd_50000_half_map_1.map
AnnotationSecond half map of the consensus dimer at a pixel sitze of 3.394 Angstrom/pixel (bin2) used for symmetry expansion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half map of the consensus dimer at...

Fileemd_50000_half_map_2.map
AnnotationFirst half map of the consensus dimer at a pixel sitze of 3.394 Angstrom/pixel (bin2) used for symmetry expansion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polytomella sp.

EntireName: Polytomella sp.
Components
  • Cell: Polytomella sp.

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Supramolecule #1: Polytomella sp.

SupramoleculeName: Polytomella sp. / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Polytomella (plant)

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA PLUNGER / Details: GP2.
DetailsLiquid culture

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4040 pixel / Average electron dose: 1.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImage series were saved aligned and gain normalized
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number subtomograms used: 130721
ExtractionNumber tomograms: 255 / Number images used: 363061 / Method: template matching / Software - Name: STOPGAP
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

6rd4


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

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