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- PDB-2e5u: C-terminal domain of Epsilon subunit of F1F0-ATP synthase from th... -

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Basic information

Entry
Database: PDB / ID: 2e5u
TitleC-terminal domain of Epsilon subunit of F1F0-ATP synthase from the Thermophilic Bacillus PS3
ComponentsATP synthase epsilon chain
KeywordsHYDROLASE / ATP synthase / F1FO ATP synthase / F1-ATPase / Epsilon subunit / ATP
Function / homology
Function and homology information


proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / 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
Similarity search - Domain/homology
ATP synthase epsilon chain / ATP synthase epsilon chain
Similarity search - Component
Biological speciesBacillus sp. PS3 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYagi, H. / Akutsu, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structures of the thermophilic F1-ATPase {varepsilon} subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1
Authors: Yagi, H. / Kajiwara, N. / Tanaka, H. / Tsukihara, T. / Kato-Yamada, Y. / Yoshida, M. / Akutsu, H.
History
DepositionDec 25, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE These residues are AKERAERR instead of RKSGRTP according to Kato-Yamada Y., Yoshida M., ...SEQUENCE These residues are AKERAERR instead of RKSGRTP according to Kato-Yamada Y., Yoshida M., Hisabori T. [J.Biol.Chem. 275:35746-35750(2000).].

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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)4,7361
Polymers4,7361
Non-polymers00
Water00
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 lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide ATP synthase epsilon chain / ATP synthase F1 sector epsilon subunit


Mass: 4735.500 Da / Num. of mol.: 1 / Fragment: C-terminal domain, Residues 88-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. PS3 (bacteria) / Plasmid: pet32a / Production host: Escherichia coli (E. coli)
References: UniProt: P07678, UniProt: Q5KUJ4*PLUS, 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
1113D HACACB
1213D HA(CO)CACB
1313D HAHBCONH
1413D H(CCO)NH
1523D 15N-edited NOESY
1613D 13C-edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM TF1-Epsilon subunit U-15N, 13C; 50mM phosphate buffer K; 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM TF1-Epsilon subunit U-15N; 50mM phosphate buffer K; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 10mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.3Delaglio, F.processing
Sparky3.11Goddarddata analysis
CYANA1.0.6Guentert, P.structure solution
CYANA1.0.6Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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