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- EMDB-27312: E. coli ATP synthase imaged in 10mM MgATP State3 "down" Fo refine -

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Basic information

Entry
Database: EMDB / ID: EMD-27312
TitleE. coli ATP synthase imaged in 10mM MgATP State3 "down" Fo refine
Map data
Sample
  • Complex: ATP synthase
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsSobti M / Stewart AG
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Commun Biol / Year: 2023
Title: Changes within the central stalk of E. coli FF ATP synthase observed after addition of ATP.
Authors: Meghna Sobti / Yi C Zeng / James L Walshe / Simon H J Brown / Robert Ishmukhametov / Alastair G Stewart /
Abstract: FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to ...FF ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the F motor that is transferred to the F motor to catalyze ATP production, with flexible F/F coupling required for efficient catalysis. FF ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli FF ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the F motor. This highlights the importance of the central rotor for flexible coupling of the F and F motors and provides further insight into the regulatory mechanism mediated by subunit ε.
History
DepositionJun 14, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27312.png

Downloads & links

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Map

FileDownload / File: emd_27312.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 352 pix.
= 379.808 Å		1.08 Å/pix.
x 352 pix.
= 379.808 Å		1.08 Å/pix.
x 352 pix.
= 379.808 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.079 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.0052392124 - 0.031465583
Average (Standard dev.)-0.00015953013 (±0.00180758)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 379.80798 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27312_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_27312_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : ATP synthase

EntireName: ATP synthase
Components
  • Complex: ATP synthase

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Supramolecule #1: ATP synthase

SupramoleculeName: ATP synthase / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Escherichia coli (E. coli)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8757
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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