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- EMDB-49840: ATPase Hybrid F1 with the ancestral core domains Catalytic Dwell -

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Basic information

Entry
Database: EMDB / ID: EMD-49840
TitleATPase Hybrid F1 with the ancestral core domains Catalytic Dwell
Map dataATPase Hybrid F1 with the ancestral core domains Catalytic Dwell
Sample
  • Complex: ATPase Hybrid F1 with the ancestral core domains
    • Protein or peptide: ATPase hybrid F1 with the ancestral core domains alpha chains
    • Protein or peptide: ATPase hybrid F1 with the ancestral core domains beta chains
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsEnerygy / Ancestral ATPase / ELECTRON TRANSPORT
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase
Similarity search - Domain/homology
ATP synthase gamma chain
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria) / Pseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 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_49840.png

Downloads & links

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Map

FileDownload / File: emd_49840.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATPase Hybrid F1 with the ancestral core domains Catalytic 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: 0.15
Minimum - Maximum-0.83428735 - 1.3258376
Average (Standard dev.)0.000023892879 (±0.046717875)
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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Additional map: Additional Map

Fileemd_49840_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_49840_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_49840_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
    • Protein or peptide: ATPase hybrid F1 with the ancestral core domains alpha chains
    • Protein or peptide: ATPase hybrid F1 with the ancestral core domains beta chains
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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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-#3
Source (natural)Organism: Bacillus sp. PS3 (bacteria)

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Macromolecule #1: ATPase hybrid F1 with the ancestral core domains alpha chains

MacromoleculeName: ATPase hybrid F1 with the ancestral core domains alpha chains
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 55.987812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHHHHHHGS IRAEEISALI KQQIENYESQ IQVSDVGTVI QVGDGIARAH GLDNVMSGEL VEFANGVMGM ALNLEENNVG IVILGPYTG IKEGDEVRRT GRIMEVPVGE ELIGRVVNAL GQPIDGKGPI NAKEFRPVER KAPGVVDRQP VKEPLQTGIK A IDAMIPIG ...String:
MSHHHHHHGS IRAEEISALI KQQIENYESQ IQVSDVGTVI QVGDGIARAH GLDNVMSGEL VEFANGVMGM ALNLEENNVG IVILGPYTG IKEGDEVRRT GRIMEVPVGE ELIGRVVNAL GQPIDGKGPI NAKEFRPVER KAPGVVDRQP VKEPLQTGIK A IDAMIPIG RGQRELIIGD RQTGKTAIAI DTIINQKGQD VICIYVAIGQ KQSTVAQVVK TLEEHGAMEY TIVVAATASD PA ALQYIAP YAGCAMGEYF RDKGKHALVV YDDLSKHAVA YRQISLLLRR PPGREAYPGD VFYLHSRLLE RAAKLSDEKG GGS LTALPI IETQAGDVSA YIPTNVISIT DGQIYLESDL FYSGIRPAIN VGLSVSRVGG AAQIKAMKQV AGKLRLDLAQ YREL QAFAQ FASDLDEATR AQLERGQRMT EILKQPQYSP MPVEKQVVII YAGTNGYLDD IPVEKVKEFE DGFLEYIESK HPDIL EEIR EKKALDDELE EKLKKAIKEF KATFK

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Macromolecule #2: ATPase hybrid F1 with the ancestral core domains beta chains

MacromoleculeName: ATPase hybrid F1 with the ancestral core domains beta chains
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 53.888594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG PETLGRMFDV LGEPIDEKGP VKAKKRWPIH RPPPSLSEQS TEDEILETGI KVIDLLAPIP K GGKIGLFG ...String:
MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG PETLGRMFDV LGEPIDEKGP VKAKKRWPIH RPPPSLSEQS TEDEILETGI KVIDLLAPIP K GGKIGLFG GAGVGKTVLI MELIRNIAYE HKGFSVFAGV GERSREGNEL WLEMKESGVL DNTVLVFGQM NEPPGARFRV AL TGLTMAE YFRDEEGKDV LLFIDNIFRF AQAGSEVSAL LGRMPSEVGY QPTLATEMAE LQERITSTRR GSITSVQAIY VPA DDLTDP APATTFAHLD ATIVLSRELA EKGIYPAVDP LQSTSRIMDP RIVSEEHYEV ARRVREILQR YKDLQDIIAI LGME ELSEE DKLIVQRARK IQRFLSQPFH VAEHFTGRPG KYVPIEDTIR GFKEILDGKL DDVPEQAFYM VGTIEEAVEK AKKMK KE

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Macromolecule #3: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 31.86557 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAC PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL ...String:
MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAC PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL YMYYNHYVSA IQQEVTERKL LPLTDLAENK QRTVYEFEPS QEECLDVLLP QYAESLIYGA LLDAKASEHA AR MTAMKNA TDNANELIRT LTLSYNRARQ AAITQEITEI VAGANALQ

UniProtKB: ATP synthase gamma chain

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 1.0 µm / Nominal defocus min: 0.2 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: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 206455
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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