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- PDB-2htg: Structural and functional characterization of TM VII of the NHE1 ... -

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Basic information

Entry
Database: PDB / ID: 2htg
TitleStructural and functional characterization of TM VII of the NHE1 isoform of the Na+/H+ exchanger
ComponentsNHE1 isoform of Na+/H+ exchanger 1
KeywordsMEMBRANE PROTEIN / transmembrane segment / helix-kink-helix
Function / homology
Function and homology information


sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / sodium:proton antiporter activity ...sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / positive regulation of calcium:sodium antiporter activity / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / sodium:proton antiporter activity / positive regulation of action potential / maintenance of cell polarity / positive regulation of calcineurin-NFAT signaling cascade / regulation of pH / sodium ion export across plasma membrane / cellular response to acidic pH / cardiac muscle cell differentiation / ion binding / sodium ion import across plasma membrane / protein phosphatase 2B binding / intracellular sodium ion homeostasis / cardiac muscle cell contraction / response to acidic pH / regulation of stress fiber assembly / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of mitochondrial membrane permeability / cellular response to cold / cellular response to antibiotic / regulation of focal adhesion assembly / positive regulation of cardiac muscle hypertrophy / positive regulation of the force of heart contraction / cellular response to organic cyclic compound / intercalated disc / monoatomic ion transport / potassium ion transmembrane transport / proton transmembrane transport / T-tubule / cellular response to epinephrine stimulus / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / stem cell differentiation / regulation of intracellular pH / phospholipid binding / cellular response to mechanical stimulus / cellular response to insulin stimulus / calcium-dependent protein binding / cell migration / lamellipodium / protein complex oligomerization / protein-macromolecule adaptor activity / cellular response to hypoxia / positive regulation of cell growth / basolateral plasma membrane / membrane => GO:0016020 / molecular adaptor activity / calmodulin binding / positive regulation of apoptotic process / membrane raft / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
NHE-1 / Sodium/hydrogen exchanger 1
Similarity search - Component
MethodSOLUTION NMR / simulated annealing; torsion angle dynamics
AuthorsRainey, J.K. / Ding, J. / Xu, C. / Fliegel, L. / Sykes, B.D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and functional characterization of transmembrane segment VII of the Na(+)/H(+) exchanger isoform 1
Authors: Ding, J. / Rainey, J.K. / Xu, C. / Sykes, B.D. / Fliegel, L.
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NHE1 isoform of Na+/H+ exchanger 1


Theoretical massNumber of molelcules
Total (without water)3,0811
Polymers3,0811
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)66 / 120structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein/peptide NHE1 isoform of Na+/H+ exchanger 1 / Sodium/hydrogen exchanger 1 / NHE-1 / Solute carrier family 9 member 1 / APNH


Mass: 3080.642 Da / Num. of mol.: 1 / Fragment: Transmembrane segment VII / Source method: obtained synthetically
Details: Synthesized using solid-phase chemical peptide synthesis techniques. One unlabeled, one labeled sample (15N labels at L254, L258, G261, L264, A268, and L273)
References: UniProt: P19634, UniProt: O08938*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
13113C-natural abundance HSQC
1422D NOESY
1522D TOCSY
16213C-natural abundance HSQC
NMR detailsText: 15N labels were used to assist in assignments. 2D homonuclear NOESY data from labeled and unlabeled samples were pooled for structure calculation.

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Sample preparation

Details
Solution-IDContentsSolvent system
1~ 1 mM peptide synthetic source 1 (unlabeled), 90% H2O/10% D2O, ~ 75 mM dodecylphosphocholine, 1.0 mM DSS90% H2O/10% D2O
2~ 1 mM peptide synthetic source 2 (6 specific 15N labels), 90% H2O/10% D2O, ~ 75 mM dodecylphosphocholine, 1.0 mM DSS90% H2O/10% D2O
Sample conditionsIonic strength: ~ 75 mM Na+/DPC- / pH: 4.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
BioPackVariancollection
NMRPipe2005.319.14.56Delaglio et al.processing
Sparky3.11Goddard & Knellerdata analysis
XPLOR-NIH2.13Schwieters et al.structure solution
XPLOR-NIH2.13Schwieters et al.refinement
RefinementMethod: simulated annealing; torsion angle dynamics / Software ordinal: 1
Details: 1311 unique NOE restraints were used; 25 dihedral angle restraints. All inter-residue restraints were made ambiguous and calculations were carried out using 2 identical polypeptide chains
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 66

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