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- EMDB-61339: Engineering of ATP synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-61339
TitleEngineering of ATP synthase
Map data
Sample
  • Complex: Bacillus PS3 FoF1
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit b
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsMolecular Motor / ATP synthase / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / 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, alpha subunit nucleotide-binding domain / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / 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: 2.79 Å
AuthorsHamaguchi-Suzuki N / Ueno H / Yasuda K / Marui R / Adachi N / Senda T / Noji H / Murata T
Funding support Japan, France, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H00388 Japan
Japan Society for the Promotion of Science (JSPS)JP19H05624 Japan
Japan Society for the Promotion of Science (JSPS)JP23K18092 Japan
Human Frontier Science Program (HFSP)RGP0054/2020 France
Japan Agency for Medical Research and Development (AMED)JP23ama121013 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Engineering of ATP synthase for enhancement of proton-to-ATP ratio.
Authors: Hiroshi Ueno / Kiyoto Yasuda / Norie Hamaguchi-Suzuki / Riku Marui / Naruhiko Adachi / Toshiya Senda / Takeshi Murata / Hiroyuki Noji /
Abstract: FF-ATP synthase (FF) interconverts the energy of the proton motive force (pmf) and that of ATP through the mechanical rotation. The H/ATP ratio, one of the most crucial parameters in bioenergetics, ...FF-ATP synthase (FF) interconverts the energy of the proton motive force (pmf) and that of ATP through the mechanical rotation. The H/ATP ratio, one of the most crucial parameters in bioenergetics, varies among species due to differences in the number of H-binding c-subunits, resulting in H/ATP ratios ranging from 2.7 to 5. In this study, we seek to significantly enhance the H/ATP ratio by employing an alternative approach that differs from that of nature. We engineer FF to form multiple peripheral stalks, each bound to a proton-conducting a-subunit. The engineered FF exhibits an H/ATP ratio of 5.8, surpassing the highest ratios found in naturally occurring FFs, enabling ATP synthesis under low pmf conditions where wild-type enzymes cannot synthesize ATP. Structural analysis reveals that the engineered FF forms up to three peripheral stalks and a-subunits. This study not only provides valuable insights into the H-transport mechanism of FF but also opens up possibilities for engineering the foundation of cellular bioenergetics.
History
DepositionAug 28, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61339.png

Downloads & links

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Map

FileDownload / File: emd_61339.map.gz / Format: CCP4 / Size: 244.1 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.)
0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
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Contour LevelBy AUTHOR: 0.0439
Minimum - Maximum-0.19362275 - 0.35727122
Average (Standard dev.)0.0011786416 (±0.0133214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61339_msk_1.map
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Additional map: #1

Fileemd_61339_additional_1.map
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Half map: #2

Fileemd_61339_half_map_1.map
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Half map: #1

Fileemd_61339_half_map_2.map
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Sample components

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Entire : Bacillus PS3 FoF1

EntireName: Bacillus PS3 FoF1
Components
  • Complex: Bacillus PS3 FoF1
    • Protein or peptide: ATP synthase subunit beta
    • Protein or peptide: ATP synthase gamma chain
    • Protein or peptide: ATP synthase epsilon chain
    • Protein or peptide: ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha
    • Protein or peptide: ATP synthase subunit b
    • Protein or peptide: ATP synthase subunit b
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Bacillus PS3 FoF1

SupramoleculeName: Bacillus PS3 FoF1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4, #6, #5
Source (natural)Organism: Bacillus sp. PS3 (bacteria)

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Macromolecule #1: ATP synthase subunit beta

MacromoleculeName: ATP synthase subunit beta / 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: 53.424625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #2: ATP synthase gamma chain

MacromoleculeName: ATP synthase gamma chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 31.859523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL ...String:
MASLRDIKTR INATKKTSQI TKAMEMVSTS KLNRAEQNAK SFVPYMEKIQ EVVANVALGA GGASHPMLVS RPVKKTGYLV ITSDRGLAG AYNSNVLRLV YQTIQKRHAS PDEYAIIVIG RVGLSFFRKR NMPVILDITR LPDQPSFADI KEIARKTVGL F ADGTFDEL YMYYNHYVSA IQQEVTERKL LPLTDLAENK QRTVYEFEPS QEEILDVLLP QYAESLIYGA LLDAKASEHA AR MTAMKNA TDNANELIRT LTLSYNRARQ AAITQEITEI VAGANALQ

UniProtKB: ATP synthase gamma chain

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Macromolecule #3: ATP synthase epsilon chain

MacromoleculeName: ATP synthase epsilon chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 9.221647 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKTIHVSVVT PDGPVYEDDV EMVSVKAKSG ELGILPGHIP LVAPLEISAA RLKKGGKTQY IAVSGGFLEV RPDKVTILAQ AAERAED

UniProtKB: ATP synthase epsilon chain

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Macromolecule #4: ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthas...

MacromoleculeName: ATP synthase delta subunit,ATP synthase subunit alpha,ATP synthase subunit alpha
type: protein_or_peptide / ID: 4
Details: based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200),based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200)
Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 63.248145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGIAKAVAYS ARPLTDEELR ALSDVFAQKV GKQTLEIENI IDPELIGGVR LRIGNRIYDG SVSGQLERIR RQLIGGSGGS IRAEEISAL IKQQIENYES QIQVSDVGTV IQVGDGIARA HGLDNVMSGE LVEFANGVMG MALNLEENNV GIVILGPYTG I KEGDEVRR ...String:
MGIAKAVAYS ARPLTDEELR ALSDVFAQKV GKQTLEIENI IDPELIGGVR LRIGNRIYDG SVSGQLERIR RQLIGGSGGS IRAEEISAL IKQQIENYES QIQVSDVGTV IQVGDGIARA HGLDNVMSGE LVEFANGVMG MALNLEENNV GIVILGPYTG I KEGDEVRR TGRIMEVPVG EALIGRVVNP LGQPVDGLGP VETTETRPIE SPAPGVMDRR SVHEPLQTGI KAIDALVPIG RG QRELIIG DRQTGKTSVA IDTIINQKDQ NMISIYVAIG QKESTVRTVV ETLRKHGALD YTIVVTASAS QPAPLLFLAP YAG VAMGEY FMYKGKHVLV VYDDLSKQAA AYRELSLLLR RPPGREAYPG DIFYLHSRLL ERAAKLSDAK GGGSLTALPF VETQ AGDIS AYIPTNVISI TDGQIFLQSD LFFSGVRPAI NAGLSVSRVG GAAQIKAMKK VAGTLRLDLA AYRELEAFAQ FGSDL DKAT QAKLARGART VEVLKQDLHQ PIPVEKQVLI IYALTRGFLD DIPVEDVRRF EKEFYLFLDQ NGQHLLEHIR TTKDLP NED DLNKAIEAFK KTFVVSQ

UniProtKB: ATP synthase subunit alpha

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Macromolecule #5: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 5
Details: the same molecule as chain B,L and N; the full sequence is MGEAAHGISGGTIIYQLLMFIILLALLRKFAWQPLMNIMKQREEHIANEIDQAEKRRQEA EKLLEEQRELMKQSRQEAQALIENARKLAEEQKEQIVASARAEAERVKETAKKEIEREKE ...Details: the same molecule as chain B,L and N; the full sequence is MGEAAHGISGGTIIYQLLMFIILLALLRKFAWQPLMNIMKQREEHIANEIDQAEKRRQEA EKLLEEQRELMKQSRQEAQALIENARKLAEEQKEQIVASARAEAERVKETAKKEIEREKE QAMAALREQVASLSVLIASKVIEKELTEQDQRKLIEAYIKDVQEVGGAR
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 18.601707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGEAAHGISG GTIIYQLLMF IILLALLRKF AWQPLMNIMK QREEHIANEI DQAEKRRQEA EKLLEEQREL MKQSRQEAQA LIENARKLA EEQKEQIVAS ARAEAERVKE TAKKEIEREK EQAMAALREQ VASLSVLIAS KVI(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) ...String:
MGEAAHGISG GTIIYQLLMF IILLALLRKF AWQPLMNIMK QREEHIANEI DQAEKRRQEA EKLLEEQREL MKQSRQEAQA LIENARKLA EEQKEQIVAS ARAEAERVKE TAKKEIEREK EQAMAALREQ VASLSVLIAS KVI(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #6: ATP synthase subunit b

MacromoleculeName: ATP synthase subunit b / type: protein_or_peptide / ID: 6
Details: based on pTR19-ASDS, which was created by Suzuki et al. (doi: 10.1074/jbc.M111210200)
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Molecular weightTheoretical: 19.437396 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGEAAHGISG GTIIYQLLMF IILLALLRKF AWQPLMNIMK QREEHIANEI DQAEKRRQEA EKLLEEQREL MKQSRQEAQA LIENARKLA EEQKEQIVAS ARAEAERVKE TAKKEIEREK EQAMAALREQ VASLSVLIAS KVIEKELTEQ DQRKLIEAYI K DVQEVGGA R

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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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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 3 / Number real images: 56081 / 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: PDB ENTRY
PDB model - PDB ID:

6n2z

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 88259
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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