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- PDB-7vkv: NMR structure of the zeta-subunit of the F1F0-ATPase from Sinorhi... -

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Basic information

Entry
Database: PDB / ID: 7vkv
TitleNMR structure of the zeta-subunit of the F1F0-ATPase from Sinorhizobium meliloti
Componentszeta-subunit
KeywordsPROTEIN BINDING / soluble protein / 4 alpha-helix / F1FO-ATPase binding subunit
Function / homologyATPase inhibitor subunit zeta / ATPase inhibitor subunit zeta superfamily / ATPase inhibitor subunit zeta / Uncharacterized protein
Function and homology information
Biological speciesSinorhizobium meliloti 1021 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsYang, L.Y. / Mendoza-Hoffmann, F. / Buratto, D.
Funding support China, Mexico, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21904088 China
National Council of Science and Technology (CONACYT)770689 Mexico
CitationJournal: Front Mol Biosci / Year: 2023
Title: Inhibitory to non-inhibitory evolution of the zeta subunit of the F 1 F O -ATPase of Paracoccus denitrificans and alpha-proteobacteria as related to mitochondrial endosymbiosis.
Authors: Mendoza-Hoffmann, F. / Yang, L. / Buratto, D. / Brito-Sanchez, J. / Garduno-Javier, G. / Salinas-Lopez, E. / Uribe-Alvarez, C. / Ortega, R. / Sotelo-Serrano, O. / Cevallos, M.A. / Ramirez- ...Authors: Mendoza-Hoffmann, F. / Yang, L. / Buratto, D. / Brito-Sanchez, J. / Garduno-Javier, G. / Salinas-Lopez, E. / Uribe-Alvarez, C. / Ortega, R. / Sotelo-Serrano, O. / Cevallos, M.A. / Ramirez-Silva, L. / Uribe-Carvajal, S. / Perez-Hernandez, G. / Celis-Sandoval, H. / Garcia-Trejo, J.J.
History
DepositionOct 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
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
Revision 1.3May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
X: zeta-subunit


Theoretical massNumber of molelcules
Total (without water)11,6161
Polymers11,6161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Superdex 200 has been done to purify the whole F1FO-ATPase of Sinorhizobium meliloty, where we can find the zeta subunit attached to it on a WB. Superdex75 has been used to ...Evidence: gel filtration, Superdex 200 has been done to purify the whole F1FO-ATPase of Sinorhizobium meliloty, where we can find the zeta subunit attached to it on a WB. Superdex75 has been used to purify the recombinant zeta subunit, which was used to determine the structure by NMR.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein zeta-subunit


Mass: 11616.140 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Strain: 1021 / Gene: SMc00496
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 / References: UniProt: Q92KA6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic15D APSY CBCA(CO)NH
131isotropic14D APSY HACANH
141isotropic15D APSY (HA)CA(CO)NH
151isotropic13D 1H-13C NOESY aromatic
171isotropic13D 1H-13C NOESY aliphatic
161isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1.0 mM [U-13C; U-15N] zeta-subunit, 95% H2O/5% D2O
Label: 13C 15N_sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 1.0 mM / Component: zeta-subunit / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 50mM phosphate buffer, 100mM NaCl, 4.5 mM NaN3, 1mM EDTA
Ionic strength: 75 mM / Label: zeta-subunit / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
UNIOTorsten Herrmannchemical shift assignment
TopSpinBruker Biospincollection
UNIOTorsten Herrmannstructure calculation
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
GROMACSJohn Kerriganrefinement
CARAKeller and Wuthrichdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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