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- EMDB-25950: Yeast ATP synthase peripheral stalk without exogenous ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-25950
TitleYeast ATP synthase peripheral stalk without exogenous ATP
Map data
Sample
  • Complex: Yeast ATP synthase peripheral stalk without exogenous ATP
KeywordsF1-ATPase / ATP Synthase / Hydrolase / Nanomotor / Complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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_25950.png

Downloads & links

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Map

FileDownload / File: emd_25950.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.3075 Å
Density
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-2.742774 - 5.6550827
Average (Standard dev.)0.0033118469 (±0.12515102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 334.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25950_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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Additional map: Unsharpened map.

Fileemd_25950_additional_1.map
AnnotationUnsharpened map.
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_25950_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_25950_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Yeast ATP synthase peripheral stalk without exogenous ATP

EntireName: Yeast ATP synthase peripheral stalk without exogenous ATP
Components
  • Complex: Yeast ATP synthase peripheral stalk without exogenous ATP

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Supramolecule #1: Yeast ATP synthase peripheral stalk without exogenous ATP

SupramoleculeName: Yeast ATP synthase peripheral stalk without exogenous ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 84 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 TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 133843 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8817 / Average exposure time: 10.1 sec. / Average electron dose: 39.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 442025
Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.1.0)
Final 3D classificationNumber classes: 9 / Avg.num./class: 42000 / Software - Name: cryoSPARC (ver. 3.1.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.1.0)
Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 191939
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2hld


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT

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