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- EMDB-34756: F1 domain of FoF1-ATPase from Bacillus PS3, 90 degrees, low ATP -

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Basic information

Entry
Database: EMDB / ID: EMD-34756
TitleF1 domain of FoF1-ATPase from Bacillus PS3, 90 degrees, low ATP
Map data
Sample
  • Complex: FoF1 from Bacillus PS3
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsATP synthase F1 ATPase FoF1 / MOTOR PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / : / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal ...ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / : / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase alpha/beta chain, C terminal domain / : / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / C-terminal domain of V and A type ATP synthase / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta
Similarity search - Component
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: Nat Commun / Year: 2023
Title: Mechanism of ATP hydrolysis dependent rotation of bacterial ATP synthase.
Authors: Atsuki Nakano / Jun-Ichi Kishikawa / Kaoru Mitsuoka / Ken Yokoyama /
Abstract: F domain of ATP synthase is a rotary ATPase complex in which rotation of central γ-subunit proceeds in 120° steps against a surrounding αβ fueled by ATP hydrolysis. How the ATP hydrolysis ...F domain of ATP synthase is a rotary ATPase complex in which rotation of central γ-subunit proceeds in 120° steps against a surrounding αβ fueled by ATP hydrolysis. How the ATP hydrolysis reactions occurring in three catalytic αβ dimers are coupled to mechanical rotation is a key outstanding question. Here we describe catalytic intermediates of the F domain in FF synthase from Bacillus PS3 sp. during ATP mediated rotation captured using cryo-EM. The structures reveal that three catalytic events and the first 80° rotation occur simultaneously in F domain when nucleotides are bound at all the three catalytic αβ dimers. The remaining 40° rotation of the complete 120° step is driven by completion of ATP hydrolysis at αβ, and proceeds through three sub-steps (83°, 91°, 101°, and 120°) with three associated conformational intermediates. All sub-steps except for one between 91° and 101° associated with phosphate release, occur independently of the chemical cycle, suggesting that the 40° rotation is largely driven by release of intramolecular strain accumulated by the 80° rotation. Together with our previous results, these findings provide the molecular basis of ATP driven rotation of ATP synthases.
History
DepositionNov 16, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34756.png

Downloads & links

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Map

FileDownload / File: emd_34756.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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Contrast
Others
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: 0.00596
Minimum - Maximum-0.009579496 - 0.023457693
Average (Standard dev.)0.00007404699 (±0.001107291)
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_34756_msk_1.map
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Additional map: #1

Fileemd_34756_additional_1.map
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Half map: #1

Fileemd_34756_half_map_1.map
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Half map: #2

Fileemd_34756_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
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: FoF1 from Bacillus PS3

SupramoleculeName: FoF1 from Bacillus PS3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 530 KDa

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Macromolecule #1: ATP synthase subunit alpha

MacromoleculeName: ATP synthase subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 54.717398 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: SIRAEEISAL IKQQIENYES QIQVSDVGTV IQVGDGIARA HGLDNVMSGE LVEFANGVMG MALNLEENNV GIVILGPYTG IKEGDEVRR TGRIMEVPVG EALIGRVVNP LGQPVDGLGP VETTETRPIE SPAPGVMDRR SVHEPLQTGI KAIDALVPIG R GQRELIIG ...String:
SIRAEEISAL IKQQIENYES QIQVSDVGTV IQVGDGIARA HGLDNVMSGE LVEFANGVMG MALNLEENNV GIVILGPYTG IKEGDEVRR TGRIMEVPVG EALIGRVVNP LGQPVDGLGP VETTETRPIE SPAPGVMDRR SVHEPLQTGI KAIDALVPIG R GQRELIIG DRQTGKTSVA IDTIINQKDQ NMISIYVAIG QKESTVRTVV ETLRKHGALD YTIVVTASAS QPAPLLFLAP YA GVAMGEY FMYKGKHVLV VYDDLSKQAA AYRELSLLLR RPPGREAYPG DIFYLHSRLL ERAAKLSDAK GGGSLTALPF VET QAGDIS AYIPTNVISI TDGQIFLQSD LFFSGVRPAI NAGLSVSRVG GAAQIKAMKK VAGTLRLDLA AYRELEAFAQ FGSD LDKAT QAKLARGART VEVLKQDLHQ PIPVEKQVLI IYALTRGFLD DIPVEDVRRF EKEFYLFLDQ NGQHLLEHIR TTKDL PNED DLNKAIEAFK KTFVVSQ

UniProtKB: ATP synthase subunit alpha

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Macromolecule #2: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 53.424625 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG EVTLGRVFNV LGEPIDLEGD IPADARRDPI HRPAPKFEEL ATEVEILETG IKVVDLLAPY I KGGKIGLF ...String:
MHHHHHHHHH HMTRGRVIQV MGPVVDVKFE NGHLPAIYNA LKIQHKARNE NEVDIDLTLE VALHLGDDTV RTIAMASTDG LIRGMEVID TGAPISVPVG EVTLGRVFNV LGEPIDLEGD IPADARRDPI HRPAPKFEEL ATEVEILETG IKVVDLLAPY I KGGKIGLF GGAGVGKTVL IQELIHNIAQ EHGGISVFAG VGERTREGND LYHEMKDSGV ISKTAMVFGQ MNEPPGARMR VA LTGLTMA EYFRDEQGQD VLLFIDNIFR FTQAGSEVSA LLGRMPSAVG YQPTLATEMG QLQERITSTA KGSITSIQAI YVP ADDYTD PAPATTFSHL DATTNLERKL AEMGIYPAVD PLASTSRALA PEIVGEEHYQ VARKVQQTLQ RYKELQDIIA ILGM DELSD EDKLVVHRAR RIQFFLSQNF HVAEQFTGQP GSYVPVKETV RGFKEILEGK YDHLPEDAFR LVGRIEEVVE KAKAM GVEV

UniProtKB: ATP synthase subunit beta

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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: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 31.728328 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: ASLRDIKTRI NATKKTSQIT KAMEMVSTSK LNRAEQNAKS FVPYMEKIQE VVANVALGAG GASHPMLVSR PVKKTGYLVI TSDRGLAGA YNSNVLRLVY QTIQKRHASP DEYAIIVIGR VGLSFFRKRN MPVILDITRL PDQPSFADIK EIARKTVGLF A DGTFDELY ...String:
ASLRDIKTRI NATKKTSQIT KAMEMVSTSK LNRAEQNAKS FVPYMEKIQE VVANVALGAG GASHPMLVSR PVKKTGYLVI TSDRGLAGA YNSNVLRLVY QTIQKRHASP DEYAIIVIGR VGLSFFRKRN MPVILDITRL PDQPSFADIK EIARKTVGLF A DGTFDELY MYYNHYVSAI QQEVTERKLL PLTDLAENKQ RTVYEFEPSQ EEILDVLLPQ YAESLIYGAL LDAKASEHAA RM TAMKNAT DNANELIRTL TLSYNRARQA AITQEITEIV AGANALQ

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: 4 / 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: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / 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

Concentration10 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: 7653 / 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: 2654860
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 16437
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


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

PDB-8hh9:
F1 domain of FoF1-ATPase from Bacillus PS3, 90 degrees, low ATP

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