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- PDB-2jmx: OSCP-NT (1-120) in complex with N-terminal (1-25) alpha subunit f... -

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Basic information

Entry
Database: PDB / ID: 2jmx
TitleOSCP-NT (1-120) in complex with N-terminal (1-25) alpha subunit from F1-ATPase
Components
  • ATP synthase O subunit, mitochondrial
  • ATP synthase subunit alpha heart isoform, mitochondrial
KeywordsHYDROLASE / oscp-nt alpha-nt complex
Function / homology
Function and homology information


Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / proton-transporting ATP synthase activity, rotational mechanism / ADP binding ...Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / 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 O, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / simulated annealing
AuthorsCarbajo, R.J. / Neuhaus, D. / Kellas, F.A. / Yang, J. / Runswick, M.J. / Montgomery, M.G. / Walker, J.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: How the N-terminal Domain of the OSCP Subunit of Bovine F(1)F(o)-ATP Synthase Interacts with the N-terminal Region of an Alpha Subunit
Authors: Carbajo, R.J. / Kellas, F.A. / Yang, J.-C. / Runswick, M.J. / Montgomery, M.G. / Walker, J.E. / Neuhaus, D.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP synthase O subunit, mitochondrial
B: ATP synthase subunit alpha heart isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)15,8752
Polymers15,8752
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)30 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ATP synthase O subunit, mitochondrial / Oligomycin sensitivity conferral protein / OSCP


Mass: 13240.513 Da / Num. of mol.: 1 / Fragment: ATP synthase O subunit, residues 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ATP5O / Production host: Escherichia coli (E. coli)
References: UniProt: P13621, H+-transporting two-sector ATPase
#2: Protein/peptide ATP synthase subunit alpha heart isoform, mitochondrial / / F1-ATPASE


Mass: 2634.889 Da / Num. of mol.: 1
Fragment: ATP synthase subunit alpha heart isoform, residues 1-25
Source method: obtained synthetically
Details: The ATP synthase subunit alpha heart isoform is naturally found in Bos taurus.
References: UniProt: P19483, H+-transporting two-sector ATPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C, U-99% 15N] oscp-nt, 1.5 mM alpha-nt, 20 mM sodium phosphate, pH 6.5, 0.5 M NaCl, 0.001% PMSF 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMoscp-nt[U-99% 13C; U-99% 15N]1
1.5 mMalpha-nt1
Sample conditionsIonic strength: 0.5 / pH: 6.5 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpinBruker Biospincollection
SparkyGoddarddata analysis
X-PLOR3.851Brungerstructure solution
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 30

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