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- EMDB-50001: Structure of the peripheral stalk of the Polytomella ATPsynthase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50001
TitleStructure of the peripheral stalk of the Polytomella ATPsynthase dimer in whole cells
Map data
Sample
  • Cell: Polytomella sp.
KeywordsATP synthesis / in situ / OXPHOS / MEMBRANE PROTEIN
Biological speciesPolytomella sp. Pringsheim 198.80 (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 6.9 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_50001.png

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Map

FileDownload / File: emd_50001.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 460 pix.
= 749.8 Å		1.63 Å/pix.
x 460 pix.
= 749.8 Å		1.63 Å/pix.
x 460 pix.
= 749.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00455
Minimum - Maximum-0.0050242743 - 0.011463065
Average (Standard dev.)0.00003461247 (±0.0005338584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 749.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50001_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_50001_half_map_2.map
Projections & Slices
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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 sp. Pringsheim 198.80 (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 was saved aligned and gain normalized
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp / Number subtomograms used: 238622
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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