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- EMDB-9346: E. coli ATP synthase after incubation with ATP - State B -

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Basic information

Entry
Database: EMDB / ID: EMD-9346
TitleE. coli ATP synthase after incubation with ATP - State B
Map dataE. coli ATP synthase after incubation with ATP
Sample
  • Complex: E. coli ATP synthase
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsSobit M / Stewart AG
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (Australia)APP1146403 Australia
CitationJournal: Elife / Year: 2019
Title: Cryo-EM reveals distinct conformations of ATP synthase on exposure to ATP.
Authors: Meghna Sobti / Robert Ishmukhametov / James C Bouwer / Anita Ayer / Cacang Suarna / Nicola J Smith / Mary Christie / Roland Stocker / Thomas M Duncan / Alastair G Stewart /
Abstract: ATP synthase produces the majority of cellular energy in most cells. We have previously reported cryo-EM maps of autoinhibited ATP synthase imaged without addition of nucleotide (Sobti et al. 2016), ...ATP synthase produces the majority of cellular energy in most cells. We have previously reported cryo-EM maps of autoinhibited ATP synthase imaged without addition of nucleotide (Sobti et al. 2016), indicating that the subunit ε engages the α, β and γ subunits to lock the enzyme and prevent functional rotation. Here we present multiple cryo-EM reconstructions of the enzyme frozen after the addition of MgATP to identify the changes that occur when this ε inhibition is removed. The maps generated show that, after exposure to MgATP, ATP synthase adopts a different conformation with a catalytic subunit changing conformation substantially and the ε C-terminal domain transitioning via an intermediate 'half-up' state to a condensed 'down' state. This work provides direct evidence for unique conformational states that occur in ATP synthase when ATP binding prevents the ε C-terminal domain from entering the inhibitory 'up' state.
History
DepositionNov 14, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseApr 17, 2019-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.344
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.344
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9346.png

Downloads & links

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Map

FileDownload / File: emd_9346.map.gz / Format: CCP4 / Size: 303.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli ATP synthase after incubation with ATP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 430 pix.
= 421.4 Å		0.98 Å/pix.
x 430 pix.
= 421.4 Å		0.98 Å/pix.
x 430 pix.
= 421.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.98 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.344 / Movie #1: 0.344
Minimum - Maximum-0.68324375 - 1.9443973
Average (Standard dev.)0.0030602892 (±0.066410445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions430430430
Spacing430430430
CellA=B=C: 421.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.980.980.98
M x/y/z430430430
origin x/y/z0.0000.0000.000
length x/y/z421.400421.400421.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-19-94-60
NX/NY/NZ114128118
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS430430430
D min/max/mean-0.6831.9440.003

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Supplemental data

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Sample components

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Entire : E. coli ATP synthase

EntireName: E. coli ATP synthase
Components
  • Complex: E. coli ATP synthase

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Supramolecule #1: E. coli ATP synthase

SupramoleculeName: E. coli ATP synthase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 532 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

BufferpH: 8
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45446
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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