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- EMDB-33251: Nucleotide-depleted F1 domain of FoF1-ATPase from Bacillus PS3, state1 -

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Basic information

Entry
Database: EMDB / ID: EMD-33251
TitleNucleotide-depleted F1 domain of FoF1-ATPase from Bacillus PS3, state1
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
    • Protein or peptide: ATP synthase epsilon chain
  • Ligand: HYDROGENPHOSPHATE ION
KeywordsATP synthase F1 ATPase FoF1 / MOTOR PROTEIN
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / 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, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / 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: 3.1 Å
AuthorsNakano A / Kishikawa J / Nakanishi A / 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: PNAS Nexus / Year: 2022
Title: Structural basis of unisite catalysis of bacterial FF-ATPase.
Authors: Atsuki Nakano / Jun-Ichi Kishikawa / Atsuko Nakanishi / Kaoru Mitsuoka / Ken Yokoyama /
Abstract: Adenosine triphosphate (ATP) synthases (FF-ATPases) are crucial for all aerobic organisms. F, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the ...Adenosine triphosphate (ATP) synthases (FF-ATPases) are crucial for all aerobic organisms. F, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central rotor inside a cylinder made of in three different conformations (referred to as , , and ). In this study, we determined multiple cryo-electron microscopy structures of bacterial FF exposed to different reaction conditions. The structures of nucleotide-depleted FF indicate that the ε subunit directly forces to adopt a closed form independent of the nucleotide binding to . The structure of FF under conditions that permit only a single catalytic subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on instead of , where ATP hydrolysis proceeds in the steady-state catalysis of FF. This indicates that the unisite catalysis of bacterial FF significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft.
History
DepositionApr 19, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33251.png

Downloads & links

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Map

FileDownload / File: emd_33251.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.01 Å
Density
Contour LevelBy AUTHOR: 0.0067
Minimum - Maximum-0.009291622 - 0.03205847
Average (Standard dev.)0.000078422905 (±0.0011952833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 363.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33251_msk_1.map
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Additional map: #1

Fileemd_33251_additional_1.map
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Half map: #2

Fileemd_33251_half_map_1.map
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Half map: #1

Fileemd_33251_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
    • Protein or peptide: ATP synthase epsilon chain
  • Ligand: HYDROGENPHOSPHATE ION

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Supramolecule #1: FoF1 from Bacillus PS3

SupramoleculeName: FoF1 from Bacillus PS3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: 54.848598 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESPAPGVMDR RSVHEPLQTG IKAIDALVPI G RGQRELII ...String:
MSIRAEEISA LIKQQIENYE SQIQVSDVGT VIQVGDGIAR AHGLDNVMSG ELVEFANGVM GMALNLEENN VGIVILGPYT GIKEGDEVR RTGRIMEVPV GEALIGRVVN PLGQPVDGLG PVETTETRPI ESPAPGVMDR RSVHEPLQTG IKAIDALVPI G RGQRELII GDRQTGKTSV AIDTIINQKD QNMISIYVAI GQKESTVRTV VETLRKHGAL DYTIVVTASA SQPAPLLFLA PY AGVAMGE YFMYKGKHVL VVYDDLSKQA AAYRELSLLL RRPPGREAYP GDIFYLHSRL LERAAKLSDA KGGGSLTALP FVE TQAGDI SAYIPTNVIS ITDGQIFLQS DLFFSGVRPA INAGLSVSRV GGAAQIKAMK KVAGTLRLDL AAYRELEAFA QFGS DLDKA TQAKLARGAR TVEVLKQDLH QPIPVEKQVL IIYALTRGFL DDIPVEDVRR FEKEFYLFLD QNGQHLLEHI RTTKD LPNE DDLNKAIEAF KKTFVVSQ

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: 31.859523 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
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 #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: 14.585905 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MKTIHVSVVT PDGPVYEDDV EMVSVKAKSG ELGILPGHIP LVAPLEISAA RLKKGGKTQY IAVSGGFLEV RPDKVTILAQ AAERAEDID VLRAKAAKER AERRLQSQQD DIDFKRAELA LKRAMNRLSV AEMK

UniProtKB: ATP synthase epsilon chain

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Macromolecule #5: HYDROGENPHOSPHATE ION

MacromoleculeName: HYDROGENPHOSPHATE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: PI
Molecular weightTheoretical: 95.979 Da
Chemical component information

ChemComp-PI:
HYDROGENPHOSPHATE ION / Phosphate

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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
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9625 / Average electron dose: 50.0 e/Å2

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Image processing

Particle selectionNumber selected: 1381269
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 201220
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-7xkh:
Nucleotide-depleted F1 domain of FoF1-ATPase from Bacillus PS3, state1

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