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- EMDB-39174: Non-catalytic site depleted and epsilon C-terminal domain deleted... -

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Basic information

Entry
Database: EMDB / ID: EMD-39174
TitleNon-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,state2,under ATP saturated condition
Map data
Sample
  • Complex: FoF1 from Bacillus sp. PS3
KeywordsComplex / MEMBRANE PROTEIN
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKobayashi R / Nakano A / Mitsuoka K / Yokoyama K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Other government23H03231 Japan
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2025
Title: ADP-inhibited structure of non-catalytic site-depleted FF-ATPase from thermophilic Bacillus sp. PS-3.
Authors: Ren Kobayashi / Astuki Nakano / Kaoru Mitsuoka / Ken Yokoyama /
Abstract: The F domain of FF-ATP synthases/ATPases (FF) possesses three catalytic sites on the three αβ interfaces, termed αβ, αβ, and αβ, located mainly on the β subunits. The enzyme also has three ...The F domain of FF-ATP synthases/ATPases (FF) possesses three catalytic sites on the three αβ interfaces, termed αβ, αβ, and αβ, located mainly on the β subunits. The enzyme also has three non-catalytic ATP-binding sites on the three αβ interfaces, located mainly on the α subunits. When ATP does not bind to the non-catalytic site, FF becomes significantly prone to ADP inhibition, ultimately resulting in the loss of ATPase activity. However, the underlying mechanism of ADP inhibition remains unclear. Here, we report the cryo-EM structure of the non-catalytic site-depleted (ΔNC) FF from thermophilic Bacillus sp. PS-3, which completely lacks the ability to bind ATP (and ADP) upon transitioning to the ADP-inhibited form. The structure closely resembled the 81° rotated structure of the wild-type FF, except for minor movements in the C-terminal region of the α subunit. In this structure, unlike the wild-type enzyme, the catalytic site at αβ, responsible for ATP hydrolysis, was occupied by ADP-Mg, with the absence of Pi. Furthermore, the catalytic site at αβ, where ATP enters the F domain during steady-state catalysis, is occupied by ADP, seemingly impeding further ATP binding to the enzyme. The structure suggests that the ADP-inhibited form of the F domain is more likely due to differences in the nucleotide-binding states at the catalytic sites rather than structural differences.
History
DepositionFeb 20, 2024-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39174.png

Downloads & links

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Map

FileDownload / File: emd_39174.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
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Contour LevelBy AUTHOR: 0.0063
Minimum - Maximum-0.0075020567 - 0.028677996
Average (Standard dev.)0.00010136824 (±0.0011801084)
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_39174_msk_1.map
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Additional map: #1

Fileemd_39174_additional_1.map
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Additional map: #2

Fileemd_39174_additional_2.map
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Half map: #1

Fileemd_39174_half_map_1.map
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Half map: #2

Fileemd_39174_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
Source (natural)Organism: Bacillus sp. PS3 (bacteria)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: This study
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 60305
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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