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- EMDB-49842: ATPase hybrid F1 with the ancestral core domains Tetramer with st... -

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Basic information

Entry
Database: EMDB / ID: EMD-49842
TitleATPase hybrid F1 with the ancestral core domains Tetramer with stalk Binding Dwell
Map dataATPase hybrid F1 with the ancestral core domains Tetramer with stalk Binding Dwell
Sample
  • Complex: ATPase Hybrid F1 with the ancestral core domains
KeywordsEnerygy / Cryo-EM / single particle / Ancestral ATPase / ELECTRON TRANSPORT
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.46 Å
AuthorsStewart AG / Noji H / Sobti M / Suzuki AK
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Protein Sci / Year: 2025
Title: Functional and structural characterization of F-ATPase with common ancestral core domains in stator ring.
Authors: Aya K Suzuki / Ryutaro Furukawa / Meghna Sobti / Simon H J Brown / Alastair G Stewart / Satoshi Akanuma / Hiroshi Ueno / Hiroyuki Noji /
Abstract: Extant F-ATPases exhibit diverse rotational stepping behaviors-3-, 6-, or 9-step cycles-yet the evolutionary origin of these patterns remains unclear. Here, we used ancestral sequence reconstruction ...Extant F-ATPases exhibit diverse rotational stepping behaviors-3-, 6-, or 9-step cycles-yet the evolutionary origin of these patterns remains unclear. Here, we used ancestral sequence reconstruction to infer the catalytic β and non-catalytic α subunits of a putative ancestral F-ATPase. We then fused their functionally critical domains into the thermostable F from Bacillus PS3, yielding a stable chimeric enzyme. Cryo-EM revealed two distinct conformational states-binding and catalytic dwell states-separated by a ~34° rotation of the γ subunit, suggesting a fundamental six-step mechanism akin to that of extant six-stepping F-ATPases. Single-molecule rotation assays with ATP and the slowly hydrolyzed ATP analog ATPγS demonstrated that the chimeric motor is intrinsically a six-stepper, pausing at binding and catalytic dwell positions separated by 32.1°, although the binding dwell is significantly prolonged by an unknown mechanism. These findings indicate that F-ATPase was originally a six-stepper and diversified into 3-, 6- and 9-step forms in evolutionary adaptation. Based on these results, we discuss plausible features of the entire FF complex, along with potential physiological contexts in the last universal common ancestor and related lineages.
History
DepositionMar 20, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49842.png

Downloads & links

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Map

FileDownload / File: emd_49842.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATPase hybrid F1 with the ancestral core domains Tetramer with stalk Binding Dwell
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-1.322276 - 1.6702044
Average (Standard dev.)-0.00061966246 (±0.047358334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_49842_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_49842_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATPase Hybrid F1 with the ancestral core domains

EntireName: ATPase Hybrid F1 with the ancestral core domains
Components
  • Complex: ATPase Hybrid F1 with the ancestral core domains

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Supramolecule #1: ATPase Hybrid F1 with the ancestral core domains

SupramoleculeName: ATPase Hybrid F1 with the ancestral core domains / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 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: 0.5 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: PDB ENTRY
PDB model - PDB ID:

7l1q

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 407761
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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