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- EMDB-25941: Yeast ATP synthase F1 region State 2binding beta_tight open witho... -

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Basic information

Entry
Database: EMDB / ID: EMD-25941
TitleYeast ATP synthase F1 region State 2binding beta_tight open without exogenous ATP
Map data
Sample
  • Complex: Yeast ATP synthase F1 region State 2binding beta_tight open without exogenous ATP
KeywordsF1-ATPase / ATP Synthase / Hydrolase / Nanomotor / Complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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
CitationJournal: 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.
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_25941.png

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Map

FileDownload / File: emd_25941.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.)
1.31 Å/pix.
x 256 pix.
= 334.72 Å		1.31 Å/pix.
x 256 pix.
= 334.72 Å		1.31 Å/pix.
x 256 pix.
= 334.72 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3075 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-3.7153246 - 6.3545046
Average (Standard dev.)0.004277597 (±0.20959146)
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_25941_msk_1.map
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Additional map: Unsharpened map.

Fileemd_25941_additional_1.map
AnnotationUnsharpened map.
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Half map: #1

Fileemd_25941_half_map_1.map
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Half map: #2

Fileemd_25941_half_map_2.map
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Sample components

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Entire : Yeast ATP synthase F1 region State 2binding beta_tight open witho...

EntireName: Yeast ATP synthase F1 region State 2binding beta_tight open without exogenous ATP
Components
  • Complex: Yeast ATP synthase F1 region State 2binding beta_tight open without exogenous ATP

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Supramolecule #1: Yeast ATP synthase F1 region State 2binding beta_tight open witho...

SupramoleculeName: Yeast ATP synthase F1 region State 2binding beta_tight open without exogenous ATP
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: USY006
Molecular weightTheoretical: 400 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
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
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 FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 442025
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1.0) / Number images used: 57468
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.1.0)
Final 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)
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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