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- PDB-7wem: Solid-state NMR Structure of TFo c-Subunit Ring -

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Basic information

Entry
Database: PDB / ID: 7wem
TitleSolid-state NMR Structure of TFo c-Subunit Ring
ComponentsATP synthase subunit c
KeywordsPROTON TRANSPORT / decamer helices ring in membrane ATP synthase rotor
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
Similarity search - Function
ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
ATP synthase subunit c
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
MethodSOLID-STATE NMR / simulated annealing
AuthorsAkutsu, H. / Todokoro, Y. / Kang, S.-J. / Suzuki, T. / Yoshida, M. / Ikegami, T. / Fujiwara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Chemical Conformation of the Essential Glutamate Site of the c -Ring within Thermophilic Bacillus F o F 1 -ATP Synthase Determined by Solid-State NMR Based on its Isolated c -Ring Structure.
Authors: Todokoro, Y. / Kang, S.J. / Suzuki, T. / Ikegami, T. / Kainosho, M. / Yoshida, M. / Fujiwara, T. / Akutsu, H.
History
DepositionDec 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP synthase subunit c
B: ATP synthase subunit c
C: ATP synthase subunit c
D: ATP synthase subunit c
E: ATP synthase subunit c
F: ATP synthase subunit c
G: ATP synthase subunit c
H: ATP synthase subunit c
I: ATP synthase subunit c
J: ATP synthase subunit c


Theoretical massNumber of molelcules
Total (without water)73,88910
Polymers73,88910
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area29830 Å2
ΔGint-308 kcal/mol
Surface area26270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10010 structures for lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
ATP synthase subunit c / / ATP synthase F(0) sector subunit c / F-type ATPase subunit c / F-ATPase subunit c / Lipid-binding protein


Mass: 7388.850 Da / Num. of mol.: 10 / Mutation: S2H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Strain: PS3 / Gene: atpE, uncE / Production host: Escherichia coli (E. coli) / References: UniProt: P00845

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 13C DARR
121isotropic22D 13C DARR

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Sample preparation

DetailsType: liposome
Contents: 83 ug/uL 13C ATP synthase c-subunit ring, solid-state
Label: 13C-sample / Solvent system: solid-state
SampleConc.: 83 ug/uL / Component: ATP synthase c-subunit ring / Isotopic labeling: 13C
Sample conditionsDetails: frozen / Ionic strength: 10 mM / Label: conditions 1 / pH: 7.5 pD / Pressure: ambient atm / Temperature: 233 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Infinity plusVarianInfinity plus6001
Varian Infinity plusVarianInfinity plus7002

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Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Xplor-NIH with an energy function EEFx
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 10 structures for lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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