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- EMDB-34771: FoF1-ATPase from Bacillus PS3,120 degrees,state1,highATP -

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Basic information

Entry
Database: EMDB / ID: EMD-34771
TitleFoF1-ATPase from Bacillus PS3,120 degrees,state1,highATP
Map data
Sample
  • Complex: FoF1 from Bacillus PS3
KeywordsATP synthase F1 ATPase FoF1 / MOTOR PROTEIN
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNakano A / Kishikawa J / 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: To Be Published
Title: Single-particle cryo-EM reveals the chemical-mechanical cycle of fof1 driven by ATP hydrolysis.
Authors: Nakano A / Yokoyama K / Kishikawa J / Nakanishi A / Mitsuoka K
History
DepositionNov 16, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34771.png

Downloads & links

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Map

FileDownload / File: emd_34771.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å		0.88 Å/pix.
x 360 pix.
= 316.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.013277281 - 0.029693648
Average (Standard dev.)-0.00007545324 (±0.0016526259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_34771_msk_1.map
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Additional map: #1

Fileemd_34771_additional_1.map
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Half map: #1

Fileemd_34771_half_map_1.map
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Half map: #2

Fileemd_34771_half_map_2.map
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Sample components

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Entire : FoF1 from Bacillus PS3

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

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Supramolecule #1: FoF1 from Bacillus PS3

SupramoleculeName: FoF1 from Bacillus PS3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
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

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5922 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.03843 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1118093
Startup modelType of model: INSILICO MODEL
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 5866
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6n2y

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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