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- EMDB-39284: F1 domain of Non-catalytic site depleted and epsilon C-terminal d... -

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Basic information

Entry
Database: EMDB / ID: EMD-39284
TitleF1 domain of Non-catalytic site depleted and epsilon C-terminal domain deleted FoF1-ATPase from Bacillus PS3,under ATP saturated condition
Map data
Sample
  • Complex: FoF1 from Bacillus sp. PS3
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsComplex / 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 delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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 / ATP synthase epsilon chain
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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 27, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39284.png

Downloads & links

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Map

FileDownload / File: emd_39284.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00751
Minimum - Maximum-0.009590233 - 0.037719
Average (Standard dev.)0.00006104336 (±0.0011360567)
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_39284_msk_1.map
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Additional map: #1

Fileemd_39284_additional_1.map
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Additional map: #2

Fileemd_39284_additional_2.map
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Half map: #1

Fileemd_39284_half_map_1.map
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Half map: #2

Fileemd_39284_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
    • Protein or peptide: ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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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-#4
Source (natural)Organism: Bacillus sp. PS3 (bacteria)

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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: 51.699117 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: SDVGTVIQVG DGIARAHGLD NVMSGELVEF ANGVMGMALN LEENNVGIVI LGPYTGIKEG DEVRRTGRIM EVPVGEALIG RVVNPLGQP VDGLGPVETT ETRPIESRAP GVMDRRSVHE PLQTGIKAID ALVPIGRGQR ELIIGDRQTG AASVAIDTII N QKDQNMIS ...String:
SDVGTVIQVG DGIARAHGLD NVMSGELVEF ANGVMGMALN LEENNVGIVI LGPYTGIKEG DEVRRTGRIM EVPVGEALIG RVVNPLGQP VDGLGPVETT ETRPIESRAP GVMDRRSVHE PLQTGIKAID ALVPIGRGQR ELIIGDRQTG AASVAIDTII N QKDQNMIS IYVAIGQKES TVRTVVETLR KHGALDYTIV VTASASQPAP LLFLAPYAGV AMGEYFMYKG KHVLVVYAAL SK QAAAYRE LSLLLRRPPG REAYPGDIFY LHSRLLERAA KLSDAKGGGS LTALPFVETQ AGDISAYIPT NVISITDGQI FLQ SDLFFS GVRPAINAGL SVSRVGGAAQ IKAMKKVAGT LRLDLAAYRE LEAFAQFGSD LDKATQAKLA RGARTVEVLK QDLH QPIPV EKQVLIIYAL TRGFLDDIPV EDVRRFEKEF YLFLDQNGQH LLEHIRTTKD LPNEDDLNKA IEAFKKTFVV S

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: 51.683727 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI ...String:
MTRGRVIQVM GPVVDVKFEN GHLPAIYNAL KIQHKARNEN EVDIDLTLEV ALHLGDDTVR TIAMASTDGL IRGMEVIDTG APISVPVGE VTLGRVFNVL GEPIDLEGDI PADARRDPIH RPAPKFEELA TEVEILETGI KVVDLLAPYI KGGKIGLFGG A GVGKTVLI QELIHNIAQE HGGISVFAGV GERTREGNDL YHEMKDSGVI SKTAMVFGQM NEPPGARMRV ALTGLTMAEY FR DEQGQDV LLFIDNIFRF TQAGSEVSAL LGRMPSAVGY QPTLATEMGQ LQERITSTAK GSITSIQAIY VPADDYTDPA PAT TFSHLD ATTNLERKLA EMGIYPAVDP LASTSRALAP EIVGEEHYQV ARKVQQTLQR YKELQDIIAI LGMDELSDED KLVV HRARR IQFFLSQNFH VAEQFTGQPG SYVPVKETVR GFKEILEGKY DHLPEDAFRL VGRIEEVVEK AKAMGV

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: 31.53517 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: SLRDIKTRIN ATKKTSQITK AMEMVSTSKL NRAEQNAKSF VPYMEKIQEV VANVALGAGG ASHPMLVSRP VKKTGYLVIT SDRGLAGAY NSNVLRLVYQ TIQKRHACPD EYAIIVIGRV GLSFFRKRNM PVILDITRLP DQPSFADIKE IARKTVGLFA D GTFDELYM ...String:
SLRDIKTRIN ATKKTSQITK AMEMVSTSKL NRAEQNAKSF VPYMEKIQEV VANVALGAGG ASHPMLVSRP VKKTGYLVIT SDRGLAGAY NSNVLRLVYQ TIQKRHACPD EYAIIVIGRV GLSFFRKRNM PVILDITRLP DQPSFADIKE IARKTVGLFA D GTFDELYM YYNHYVSAIQ QEVTERKLLP LTDLAENKQR TVYEFEPSQE ECLDVLLPQY AESLIYGALL DAKASEHAAR MT AMKNATD NANELIRTLT LSYNRARQAA ITQEITEIVA GANAL

UniProtKB: ATP synthase gamma chain

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Macromolecule #4: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 9.221647 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKTIHVSVVT PDGPVYEDDV EMVSVKAKSG ELGILPGHIP LVAPLEISAA RLKKGGKTQY IAVSGGFLEV RPDKVTILAQ AAERAED

UniProtKB: ATP synthase epsilon chain

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / 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: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, 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: 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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 109111
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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