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- PDB-1mo8: ATPase -

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Basic information

Entry
Database: PDB / ID: 1mo8
TitleATPase
ComponentsSodium/Potassium-Transporting ATPase alpha-1
KeywordsHYDROLASE / six-stranded / twisted beta sheet
Function / homology
Function and homology information


energy coupled proton transmembrane transport, against electrochemical gradient / negative regulation of glucocorticoid biosynthetic process / Ion transport by P-type ATPases / positive regulation of heart contraction / Na+/K+-exchanging ATPase / P-type potassium transmembrane transporter activity / positive regulation of striated muscle contraction / response to glycoside / sodium ion homeostasis / steroid hormone binding ...energy coupled proton transmembrane transport, against electrochemical gradient / negative regulation of glucocorticoid biosynthetic process / Ion transport by P-type ATPases / positive regulation of heart contraction / Na+/K+-exchanging ATPase / P-type potassium transmembrane transporter activity / positive regulation of striated muscle contraction / response to glycoside / sodium ion homeostasis / steroid hormone binding / membrane repolarization / P-type sodium:potassium-exchanging transporter activity / sodium ion binding / sodium:potassium-exchanging ATPase complex / negative regulation of heart contraction / establishment or maintenance of transmembrane electrochemical gradient / regulation of the force of heart contraction / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / membrane hyperpolarization / intracellular sodium ion homeostasis / osmosensory signaling pathway / regulation of cardiac muscle cell contraction / relaxation of cardiac muscle / ankyrin binding / sodium ion transport / cellular response to steroid hormone stimulus / Ion homeostasis / heart contraction / phosphatase activity / potassium ion import across plasma membrane / organelle membrane / potassium ion binding / intercalated disc / lateral plasma membrane / sperm flagellum / phosphatidylinositol 3-kinase binding / cardiac muscle contraction / regulation of sodium ion transport / proton transmembrane transport / T-tubule / caveola / potassium ion transport / sarcolemma / transmembrane transport / ADP binding / regulation of blood pressure / cellular response to mechanical stimulus / melanosome / protein-folding chaperone binding / basolateral plasma membrane / postsynaptic density / endosome / response to xenobiotic stimulus / apical plasma membrane / protein heterodimerization activity / protein domain specific binding / axon / protein kinase binding / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / plasma membrane
Similarity search - Function
Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase ...Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / 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 / Cation transport ATPase (P-type) / E1-E2 ATPase / 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 / HAD superfamily / HAD-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Sodium/potassium-transporting ATPase subunit alpha-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / Automated NOESY cross peak assignment
AuthorsHilge, M. / Siegal, G. / Vuister, G.W. / Guentert, P. / Gloor, S.M. / Abrahams, J.P.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: ATP-induced conformational changes of the nucleotide-binding domain of Na,K-ATPase
Authors: Hilge, M. / Siegal, G. / Vuister, G.W. / Guentert, P. / Gloor, S.M. / Abrahams, J.P.
History
DepositionSep 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: 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: Sodium/Potassium-Transporting ATPase alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3762
Polymers23,8691
Non-polymers5071
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 / 200structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Sodium/Potassium-Transporting ATPase alpha-1 / sodium pump / Na+/K+ ATPase 1


Mass: 23869.131 Da / Num. of mol.: 1 / Fragment: residues 383-595
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06685, EC: 3.6.3.9
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: Stereospecific assignments of valine and leucine methyl groups were obtained by analysis of an 1H,13C CT HSQC spectrum on a 10% 13C-labelled sample

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Sample preparation

Details
Solution-IDContentsSolvent system
1ATPase95% H20 5% D20
2ATP95% H20 5% D20
Sample conditionsIonic strength: 20mM Tris-HCl, 0.02% NaN3 / pH: 8.6 / Pressure: ambient / Temperature: 296 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 spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1Delaglio, F. et al.processing
XEASY1.3.11Bartels, C. et al.data analysis
CYANA1.0.5http://www.guentert.comstructure solution
OPALp1Koradi, R., Billeter, M., Guentert, P.refinement
RefinementMethod: Automated NOESY cross peak assignment / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 200 / Conformers submitted total number: 20

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