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- EMDB-33252: Nucleotide-depleted F1 domain of FoF1-ATPase from Bacillus PS3, ,... -

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Basic information

Entry
Database: EMDB / ID: EMD-33252
TitleNucleotide-depleted F1 domain of FoF1-ATPase from Bacillus PS3, , state2
Map data
Sample
  • Complex: FoF1 from Bacillus sp. PS3
KeywordsATP synthase F1 ATPase FoF1 / MOTOR PROTEIN
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsNakano A / Kishikawa J / Nakanishi A / Mitsuoka K / Yokoyama K
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03231 Japan
Japan Society for the Promotion of Science (JSPS)20K06514 Japan
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
Japan Society for the Promotion of Science (JSPS)20J00162 Japan
CitationJournal: PNAS Nexus / Year: 2022
Title: Structural basis of unisite catalysis of bacterial FF-ATPase.
Authors: Atsuki Nakano / Jun-Ichi Kishikawa / Atsuko Nakanishi / Kaoru Mitsuoka / Ken Yokoyama /
Abstract: Adenosine triphosphate (ATP) synthases (FF-ATPases) are crucial for all aerobic organisms. F, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the ...Adenosine triphosphate (ATP) synthases (FF-ATPases) are crucial for all aerobic organisms. F, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central rotor inside a cylinder made of in three different conformations (referred to as , , and ). In this study, we determined multiple cryo-electron microscopy structures of bacterial FF exposed to different reaction conditions. The structures of nucleotide-depleted FF indicate that the ε subunit directly forces to adopt a closed form independent of the nucleotide binding to . The structure of FF under conditions that permit only a single catalytic subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on instead of , where ATP hydrolysis proceeds in the steady-state catalysis of FF. This indicates that the unisite catalysis of bacterial FF significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft.
History
DepositionApr 19, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33252.png

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Map

FileDownload / File: emd_33252.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.01 Å
Density
Contour LevelBy AUTHOR: 0.0086
Minimum - Maximum-0.011376596 - 0.034949142
Average (Standard dev.)0.00007814673 (±0.0012768682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 363.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33252_msk_1.map
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AxesZYX

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Additional map: #1

Fileemd_33252_additional_1.map
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Half map: #1

Fileemd_33252_half_map_1.map
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Half map: #2

Fileemd_33252_half_map_2.map
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Sample components

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Entire : FoF1 from Bacillus sp. PS3

EntireName: FoF1 from Bacillus sp. PS3
Components
  • Complex: FoF1 from Bacillus sp. PS3

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Supramolecule #1: FoF1 from Bacillus sp. PS3

SupramoleculeName: FoF1 from Bacillus sp. PS3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 530 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9625 / Average electron dose: 50.0 e/Å2

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Image processing

Particle selectionNumber selected: 1381269
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 177043
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6n2y


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

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