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- PDB-2rq6: Solution structure of the epsilon subunit of the F1-atpase from t... -

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Basic information

Entry
Database: PDB / ID: 2rq6
TitleSolution structure of the epsilon subunit of the F1-atpase from thermosynechococcus elongatus BP-1
ComponentsATP synthase epsilon chain
KeywordsHYDROLASE / ATP SYNTHASE / F1FO ATP SYNTHASE / F1-ATPASE / EPSILON SUBUNIT / ATP SYNTHESIS / CF1 / HYDROGEN ION TRANSPORT / ION TRANSPORT / MEMBRANE / THYLAKOID / TRANSPORT / CF(1)
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ATP binding
Similarity search - Function
ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / Helix hairpin bin / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / 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 / Helix Hairpins ...ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / Helix hairpin bin / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / 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 / Helix Hairpins / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ATP synthase epsilon chain
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYagi, H. / Konno, H. / Murakami-Fuse, T. / Oroguchi, H. / Akutsu, T. / Ikeguchi, M. / Hisabori, T.
CitationJournal: Biochem.J. / Year: 2010
Title: Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms.
Authors: Yagi, H. / Konno, H. / Murakami-Fuse, T. / Isu, A. / Oroguchi, T. / Akutsu, H. / Ikeguchi, M. / Hisabori, T.
History
DepositionMar 3, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase epsilon chain


Theoretical massNumber of molelcules
Total (without water)14,7651
Polymers14,7651
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1minimized average

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Components

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


Mass: 14764.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8DLG7, H+-transporting two-sector ATPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1412D 1H-1H NOESY
1513D H(CCO)NH
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D HBHA(CO)NH

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Sample preparation

DetailsContents: 1.0 mM [U-99% 15N] ATP SYNTHASE EPSILON CHAIN-1, 1.0 mM [U-99% 13C; U-99% 15N] ATP SYNTHASE EPSILON CHAIN-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMATP SYNTHASE EPSILON CHAIN-1[U-99% 15N]1
1.0 mMATP SYNTHASE EPSILON CHAIN-2[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
BRUKER DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6GUNTERT, MUMENTHALERrefinement
XwinNMRBruker Biospinstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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