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- PDB-1y4e: NMR structure of transmembrane segment IV of the NHE1 isoform of ... -

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Basic information

Entry
Database: PDB / ID: 1y4e
TitleNMR structure of transmembrane segment IV of the NHE1 isoform of the Na+/H+ exchanger
ComponentsSodium/hydrogen exchanger 1
KeywordsMEMBRANE PROTEIN / NHE1 isoform / transmembrane
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 / cardiac muscle cell differentiation / cellular response to acidic pH / sodium ion import across plasma membrane / ion binding / 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 / 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
Sodium/hydrogen exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSlepkov, E.R. / Rainey, J.K. / Li, X. / Liu, Y. / Lindhout, D.A. / Sykes, B.D. / Fliegel, L.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structural and functional characterization of transmembrane segment IV of the NHE1 isoform of the Na+/H+ exchanger.
Authors: Slepkov, E.R. / Rainey, J.K. / Li, X. / Liu, Y. / Cheng, F.J. / Lindhout, D.A. / Sykes, B.D. / Fliegel, L.
#1: Journal: Protein Sci. / Year: 2003
Title: High-yield expression of isotopically labeled peptides for use in NMR studies
Authors: Lindhout, D.A. / Thiessen, A. / Schieve, D. / Sykes, B.D.
History
DepositionNov 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/hydrogen exchanger 1


Theoretical massNumber of molelcules
Total (without water)3,1401
Polymers3,1401
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)100 / 1000structures with the lowest energy
Representative

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Components

#1: Protein/peptide Sodium/hydrogen exchanger 1 / Na+ / /H+ / exchanger 1 / NHE-1 / Na+/H+ antiporter / amiloride-sensitive / APNH


Mass: 3139.748 Da / Num. of mol.: 1 / Fragment: Transmembrane segment IV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pLysS) / References: UniProt: P19634

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
142HNHA
NMR detailsText: This structure was determined using standard 2D homonuclear techniques with the exception that HNHA J-coupling constants were incorporated.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM TM IV, unlabelled; 1 mM DSS, CDCl3:CD3OH:H2O (4:4:1 v:v:v)CDCl3:CD3OH:H2O (4:4:1 v:v:v)
22 mM TM IV, U-15N; 1 mM DSS, CDCl3:CD3OH:H2O (4:4:1 v:v:v)CDCl3:CD3OH:H2O (4:4:1 v:v:v)
Sample conditionsPressure: ambient / Temperature: 303 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
Varian INOVAVarianINOVA8001
Varian UNITYVarianUNITY6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VNMRvariousVarian Inc.collection
NMRPipe2.3Frank Delaglio, Stephan Grzesiek, Guang Zhu, Geerten W. Vuister, John Pfeifer, and Ad Baxprocessing
Sparky3.109 and 3.110T. D. Goddard and D. G. Knellerdata analysis
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 15 rounds of simulated annealing were carried out to optimize included NOE contacts and lengths, as well as J-HNHA. Finally, homoserine lactone was included. The ensemble of structures given ...Details: 15 rounds of simulated annealing were carried out to optimize included NOE contacts and lengths, as well as J-HNHA. Finally, homoserine lactone was included. The ensemble of structures given is superposed over the region I169-F176. Other useful superpositions that should be examined are D159-L163 and L165-P168.
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 100

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