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- PDB-7xkq: F1 domain of FoF1-ATPase with the down form of epsilon subunit fr... -

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Basic information

Entry
Database: PDB / ID: 7xkq
TitleF1 domain of FoF1-ATPase with the down form of epsilon subunit from Bacillus PS3
Components(ATP synthase ...) x 4
KeywordsMOTOR PROTEIN / ATP synthase F1 ATPase FoF1
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; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / Pyruvate Kinase; Chain: A, domain 1 / 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 ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / Pyruvate Kinase; Chain: A, domain 1 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit alpha / ATP synthase gamma chain / ATP synthase subunit beta / ATP synthase epsilon chain
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsNakano, A. / Kishikawa, J. / Nakanishi, A. / Mitsuoka, K. / Yokoyama, K.
Funding support Japan, 4items
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 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase gamma chain
H: ATP synthase epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,88121
Polymers371,2658
Non-polymers3,61613
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase ... , 4 types, 8 molecules ABCDEFGH

#1: Protein ATP synthase subunit alpha / ATP synthase F1 sector subunit alpha / F-ATPase subunit alpha


Mass: 54848.598 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncA, atpA / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: A0A0M3VGF9, H+-transporting two-sector ATPase
#2: Protein ATP synthase subunit beta / ATP synthase F1 sector subunit beta / F-ATPase subunit beta


Mass: 53424.625 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncD, atpD / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: A0A0M4U1P9, H+-transporting two-sector ATPase
#3: Protein ATP synthase gamma chain / ATP synthase F1 sector gamma subunit / F-ATPase gamma subunit


Mass: 31859.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncG, atpG / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0M4TPJ7
#4: Protein ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit / F-ATPase epsilon subunit


Mass: 14585.905 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Gene: uncC, atpC / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0M5MQR7

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Non-polymers , 3 types, 13 molecules

#5: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FoF1 from Bacillus sp. PS3 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 0.53 MDa / Experimental value: NO
Source (natural)Organism: Bacillus sp. PS3 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 0.0291 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9625

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4RELION4CTF correction
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10cryoSPARC3.2initial Euler assignment
11RELION4final Euler assignment
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1020321
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39991 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6N2Y

6n2y


Accession code: 6N2Y / Source name: PDB / Type: experimental model

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