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- PDB-2a7u: NMR solution structure of the E.coli F-ATPase delta subunit N-ter... -

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Basic information

Entry
Database: PDB / ID: 2a7u
TitleNMR solution structure of the E.coli F-ATPase delta subunit N-terminal domain in complex with alpha subunit N-terminal 22 residues
Components
  • ATP synthase alpha chain
  • ATP synthase delta chain
KeywordsHYDROLASE / alpha helix bundle
Function / homology
Function and homology information


proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / ATP binding / plasma membrane
Similarity search - Function
N-terminal domain of the delta subunit of the F1F0-ATP synthase / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / Peroxidase; domain 1 / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit ...N-terminal domain of the delta subunit of the F1F0-ATP synthase / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / Peroxidase; domain 1 / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP synthase subunit alpha / ATP synthase subunit delta / ATP synthase subunit delta / ATP synthase subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry; simulated annealing; molecular dynamics
Model type detailsminimized average
AuthorsWilkens, S. / Borchardt, D. / Weber, J. / Senior, A.E.
CitationJournal: Biochemistry / Year: 2005
Title: Structural Characterization of the Interaction of the delta and alpha Subunits of the Escherichia coli F(1)F(0)-ATP Synthase by NMR Spectroscopy
Authors: Wilkens, S. / Borchardt, D. / Weber, J. / Senior, A.E.
History
DepositionJul 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase alpha chain
B: ATP synthase delta chain


Theoretical massNumber of molelcules
Total (without water)17,2402
Polymers17,2402
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)1 / 10averaged minimized structure
Representativeminimized average structure

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Components

#1: Protein/peptide ATP synthase alpha chain / E.C.3.6.3.14 / F-ATPase alpha chain


Mass: 2563.966 Da / Num. of mol.: 1 / Fragment: N-terminal domain, (residues 1-22) / Source method: obtained synthetically
Details: sequence occurs naturally in E.coli, genes atpA, papA, uncA
References: UniProt: P00822, UniProt: P0ABB2*PLUS, H+-transporting two-sector ATPase
#2: Protein ATP synthase delta chain / E.C.3.6.3.14 / F-ATPase delta chain


Mass: 14676.533 Da / Num. of mol.: 1 / Fragment: N-terminal domain, (residues 2-135)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: atpH, papE, uncH / Production host: Escherichia coli (E. coli) / Strain (production host): 594
References: UniProt: P0ABA4, UniProt: P0ABA5*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 15N-separated NOESY
12113C/12C filtered 2-D NOESY
13112C/12C filtered 2-D NOESY
14114N/12C filtered 2-D NOESY

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Sample preparation

DetailsContents: 0.6 mM delta subunit N-terminal domain U-13C,15N; 0.9 mM alpha subunit N-terminal peptide; 10 mM Na,K phosphate, pH 7.2, 3mM NaN3, 0.1 mM EDTA; 93% H20, 7% D20
Solvent system: 93% H20, 7% D20
Sample conditionsIonic strength: 50 mM / pH: 7.2 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8AT Brungerstructure solution
Felix98Accelrysdata analysis
X-PLOR3.8AT Brungerrefinement
RefinementMethod: distance geometry; simulated annealing; molecular dynamics
Software ordinal: 1
Details: rms difference of non-H atoms 1.114, for the backbone atoms 0.6174
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: averaged minimized structure / Conformers calculated total number: 10 / Conformers submitted total number: 1

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