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- PDB-2kbv: Structural and functional analysis of TM XI of the NHE1 isoform o... -

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Basic information

Entry
Database: PDB / ID: 2kbv
TitleStructural and functional analysis of TM XI of the NHE1 isoform of thE NA+/H+ exchanger
ComponentsSodium/hydrogen exchanger 1
KeywordsMEMBRANE PROTEIN / transmembrane / NHE1 / micelle / Alternative splicing / Antiport / Glycoprotein / Ion transport / Membrane / Phosphoprotein / Sodium / Sodium transport / Transport
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 / potassium:proton antiporter activity / cellular response to electrical stimulus / 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 / potassium:proton antiporter activity / cellular response to electrical stimulus / sodium:proton antiporter activity / positive regulation of action potential / sodium ion export across plasma membrane / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / cardiac muscle cell differentiation / cellular response to acidic pH / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / protein phosphatase 2B binding / ion binding / regulation of stress fiber assembly / cardiac muscle cell contraction / response to acidic pH / 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 / intercalated disc / monoatomic ion transport / potassium ion transmembrane transport / cellular response to epinephrine stimulus / T-tubule / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / proton transmembrane transport / 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 / protein-macromolecule adaptor activity / protein complex oligomerization / lamellipodium / 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 / membrane / identical protein binding / 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
Model detailslowest energy, model 1
AuthorsLee, B.L. / Li, X. / Liu, Y. / Sykes, B.D. / Fliegel, L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural and Functional Analysis of Transmembrane XI of the NHE1 Isoform of the Na+/H+ Exchanger
Authors: Lee, B.L. / Li, X. / Liu, Y. / Sykes, B.D. / Fliegel, L.
History
DepositionDec 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.details ..._pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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: Sodium/hydrogen exchanger 1


Theoretical massNumber of molelcules
Total (without water)2,8861
Polymers2,8861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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: 2886.417 Da / Num. of mol.: 1 / Fragment: NHE1 transmembrane segment XI / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19634

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 150 mM DPC-1, 0.25 mM DSS-2, 2 mM TMXI-3, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
150 mMDPC-11
0.25 mMDSS-21
2 mMTMXI-31
Sample conditionspH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA6003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.19Schwieters, Kuszewski, Tjandra and Clorerefinement
VnmrJVariancollection
NMRViewJohnson, One Moon Scientificprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 10 rounds of simulated annealing and restraint refinement, followed by further rounds of refinment including dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 40

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