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- PDB-1iwf: Solution structure of the N-terminal domain of pig gastric H/K-ATPase -

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Basic information

Entry
Database: PDB / ID: 1iwf
TitleSolution structure of the N-terminal domain of pig gastric H/K-ATPase
Componentsgastric H/K-ATPase
KeywordsHYDROLASE / Fragment structure of H/K-ATPase
Function / homology
Function and homology information


H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / P-type sodium:potassium-exchanging transporter activity / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / intracellular potassium ion homeostasis / potassium ion transmembrane transport ...H+/K+-exchanging ATPase / potassium:proton exchanging ATPase complex / P-type potassium:proton transporter activity / P-type sodium:potassium-exchanging transporter activity / sodium ion export across plasma membrane / intracellular sodium ion homeostasis / potassium ion import across plasma membrane / potassium ion binding / intracellular potassium ion homeostasis / potassium ion transmembrane transport / proton transmembrane transport / apical plasma membrane / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / : / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N ...Gastric H+/K+-transporter P-type ATPase, N-terminal / Gastric H+/K+-ATPase, N terminal domain / : / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / P-type ATPase, cytoplasmic domain N / P-type ATPase actuator domain / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Potassium-transporting ATPase alpha chain 1
Similarity search - Component
MethodSOLUTION NMR / distance geometry-simulated annealing with the standard protocol of XPLOR
AuthorsFujitani, N. / Kanagawa, M. / Aizawa, T. / Ohkubo, T. / Kaya, S. / Demura, M. / Kawano, K. / Taniguchi, K. / Nitta, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2003
Title: Structure determination and conformational change induced by tyrosine phosphorylation of the N-terminal domain of the alpha-chain of pig gastric H+/K+-ATPase
Authors: Fujitani, N. / Kanagawa, M. / Aizawa, T. / Ohkubo, T. / Kaya, S. / Demura, M. / Kawano, K. / Nishimura, S. / Taniguchi, K. / Nitta, K.
History
DepositionMay 6, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: gastric H/K-ATPase


Theoretical massNumber of molelcules
Total (without water)3,6061
Polymers3,6061
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)15 / 30structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: Protein/peptide gastric H/K-ATPase / Potassium-transporting ATPase alpha chain 1


Mass: 3606.157 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Source method: obtained synthetically
Details: This peptide was synthesized containing the sequence of the N-terminal domain of pig gastric H/K-ATPase
References: UniProt: P19156, H+/K+-exchanging ATPase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2mM peptide / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 4 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglioprocessing
X-PLOR3.1Brungerrefinement
XEASYBartelsdata analysis
RefinementMethod: distance geometry-simulated annealing with the standard protocol of XPLOR
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 15

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