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- PDB-2e30: Solution structure of the cytoplasmic region of Na+/H+ exchanger ... -

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Basic information

Entry
Database: PDB / ID: 2.0E+30
TitleSolution structure of the cytoplasmic region of Na+/H+ exchanger 1 complexed with essential cofactor calcineurin B homologous protein 1
Components
  • Calcium-binding protein p22
  • Sodium/hydrogen exchanger 1
KeywordsMETAL BINDING PROTEIN/TRANSPORT PROTEIN / transporter / EF-hand / complex structure / METAL BINDING PROTEIN-TRANSPORT PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / transporter complex / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking ...negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / transporter complex / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / positive regulation of phospholipid biosynthetic process / potassium:proton antiporter activity / negative regulation of protein autophosphorylation / sodium:proton antiporter activity / positive regulation of action potential / positive regulation of protein transport / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / sodium ion export across plasma membrane / cardiac muscle cell differentiation / membrane organization / cellular response to acidic pH / sodium ion import across plasma membrane / microtubule bundle formation / protein phosphatase 2B binding / intracellular sodium ion homeostasis / response to acidic pH / regulation of stress fiber assembly / cardiac muscle cell contraction / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of mitochondrial membrane permeability / cellular response to cold / negative regulation of calcineurin-NFAT signaling cascade / cellular response to antibiotic / regulation of focal adhesion assembly / negative regulation of protein import into nucleus / negative regulation of NF-kappaB transcription factor activity / small GTPase-mediated signal transduction / positive regulation of cardiac muscle hypertrophy / protein kinase inhibitor activity / positive regulation of the force of heart contraction / cellular response to organic cyclic compound / endoplasmic reticulum-Golgi intermediate compartment / protein complex oligomerization / intercalated disc / positive regulation of protein targeting to membrane / potassium channel regulator activity / monoatomic ion transport / cytoplasmic microtubule organization / phosphatidylinositol-4,5-bisphosphate binding / transport vesicle / negative regulation of protein ubiquitination / T-tubule / potassium ion transmembrane transport / cellular response to epinephrine stimulus / response to muscle stretch / protein export from nucleus / proton transmembrane transport / negative regulation of protein phosphorylation / stem cell differentiation / regulation of intracellular pH / negative regulation of protein kinase activity / potassium ion transport / kinase binding / phospholipid binding / cellular response to insulin stimulus / cellular response to mechanical stimulus / calcium-dependent protein binding / microtubule cytoskeleton / cell migration / lamellipodium / protein-macromolecule adaptor activity / cellular response to hypoxia / microtubule binding / positive regulation of cell growth / basolateral plasma membrane / molecular adaptor activity / membrane fusion / calmodulin binding / protein stabilization / positive regulation of apoptotic process / membrane raft / apical plasma membrane / Golgi membrane / focal adhesion / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1040 / : / Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / EF hand ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1040 / : / Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / EF hand / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand / Recoverin; domain 1 / Helix non-globular / EF-hand domain pair / EF-hand, calcium binding motif / Special / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sodium/hydrogen exchanger 1 / Calcineurin B homologous protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMishima, M. / Wakabayashi, S. / Kojima, C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Solution structure of the cytoplasmic region of Na+/H+ exchanger 1 complexed with essential cofactor calcineurin B homologous protein 1
Authors: Mishima, M. / Wakabayashi, S. / Kojima, C.
History
DepositionNov 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 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: Calcium-binding protein p22
B: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5834
Polymers27,5032
Non-polymers802
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 #1lowest energy

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Components

#1: Protein Calcium-binding protein p22 / Calcium-binding protein CHP / Calcineurin homologous protein / Calcineurin B homolog


Mass: 22487.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHP1 / Plasmid: pet11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99653
#2: Protein/peptide Sodium/hydrogen exchanger 1 / Na+ / /H+ / exchanger 1 / NHE-1 / Solute carrier family 9 member 1 / Na+ / /H+ / antiporter / ...Na+ / /H+ / exchanger 1 / NHE-1 / Solute carrier family 9 member 1 / Na+ / /H+ / antiporter / amiloride- sensitive / APNH


Mass: 5015.683 Da / Num. of mol.: 1 / Fragment: NHE1 fragment (503-545)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P19634
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1233D 15N-separated NOESY
NMR detailsText: This structure was determined using hetero nuclear multidimensional NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9mM CHP1/NHE1 U-15N, U-13C, 50mM Tris buffer, 99% D2O99% D2O
20.5mM CHP1/NHE1 60%2H, U-15N, U-13C, 50mM Tris buffer, 95% H2O, 5% D2O95% H2O/5% D2O
30.9mM CHP1/NHE1 U-15N, 50mM Tris buffer, 95% H2Om, 5% D2O95% H2O/5% D2O
40.9mM CHP1/NHE1 U-15N, U-13C, 50mM Tris buffer, 95% H2O, 5% D2O95% H2O/5% D2O
50.5mM CHP1/NHE1 U-15N, 15%-13C, 50mM Tris buffer, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 30mM / pH: 6.9 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.4F. Delaglioprocessing
XPLOR-NIH2.9.6Schwieters, C.D.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 4242 distance restraints and 227 dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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