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- EMDB-25953: Yeast ATP synthase with 10 mM ATP showing strained peripheral sta... -

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Basic information

Entry
Database: EMDB / ID: EMD-25953
TitleYeast ATP synthase with 10 mM ATP showing strained peripheral stalk determined by a screening microscope
Map data
Sample
  • Complex: Yeast ATP synthase with 10 mM ATP showing strained peripheral stalk determined by a screening microscope
KeywordsF1-ATPase / ATP Synthase / Hydrolase / Nanomotor / Complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsGuo H / Rubinstein JL
Funding support Canada, 3 items
OrganizationGrant numberCountry
Canada Research ChairsElectron Cryomicroscopy Canada
Canadian Institutes of Health Research (CIHR)PJT162186 Canada
Canada Foundation for Innovation Canada
Citation
Journal: Nat Commun / Year: 2022
Title: Structure of ATP synthase under strain during catalysis.
Authors: Hui Guo / John L Rubinstein /
Abstract: ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor ...ATP synthases are macromolecular machines consisting of an ATP-hydrolysis-driven F motor and a proton-translocation-driven F motor. The F and F motors oppose each other's action on a shared rotor subcomplex and are held stationary relative to each other by a peripheral stalk. Structures of resting mitochondrial ATP synthases revealed a left-handed curvature of the peripheral stalk even though rotation of the rotor, driven by either ATP hydrolysis in F or proton translocation through F, would apply a right-handed bending force to the stalk. We used cryoEM to image yeast mitochondrial ATP synthase under strain during ATP-hydrolysis-driven rotary catalysis, revealing a large deformation of the peripheral stalk. The structures show how the peripheral stalk opposes the bending force and suggests that during ATP synthesis proton translocation causes accumulation of strain in the stalk, which relaxes by driving the relative rotation of the rotor through six sub-steps within F, leading to catalysis.
#1: Journal: Biorxiv / Year: 2022
Title: Structure of ATP synthase under strain during catalysis
Authors: Guo H / Rubinstein JL
History
DepositionJan 17, 2022-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25953.png

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Map

FileDownload / File: emd_25953.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 256 pix.
= 344.96 Å		1.35 Å/pix.
x 256 pix.
= 344.96 Å		1.35 Å/pix.
x 256 pix.
= 344.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3475 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.23676606 - 0.78670996
Average (Standard dev.)0.0024742803 (±0.06349522)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 344.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25953_msk_1.map
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Additional map: Unsharpened map.

Fileemd_25953_additional_1.map
AnnotationUnsharpened map.
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Half map: #1

Fileemd_25953_half_map_1.map
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Half map: #2

Fileemd_25953_half_map_2.map
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Sample components

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Entire : Yeast ATP synthase with 10 mM ATP showing strained peripheral sta...

EntireName: Yeast ATP synthase with 10 mM ATP showing strained peripheral stalk determined by a screening microscope
Components
  • Complex: Yeast ATP synthase with 10 mM ATP showing strained peripheral stalk determined by a screening microscope

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Supramolecule #1: Yeast ATP synthase with 10 mM ATP showing strained peripheral sta...

SupramoleculeName: Yeast ATP synthase with 10 mM ATP showing strained peripheral stalk determined by a screening microscope
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 610 KDa

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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

Concentration15 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER/RHODIUM / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 35 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 200 / Average exposure time: 15.0 sec. / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated magnification: 34483 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 0.0025 µm / Nominal defocus min: 0.001 µm / Nominal magnification: 25000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 71472
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 5919
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.15)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 2.15)
Final 3D classificationNumber classes: 4 / Avg.num./class: 6674 / Software - Name: cryoSPARC (ver. 2.15)
FSC plot (resolution estimation)

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