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- PDB-6bjf: NMR Structural and biophysical functional analysis of intracellul... -

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Basic information

Entry
Database: PDB / ID: 6bjf
TitleNMR Structural and biophysical functional analysis of intracellular loop 5 of the NHE1 isoform of the Na+/H+ exchanger.
ComponentsGLY-LEU-THR-TRP-PHE-ILE-ASN-LYS-PHE-ARG-ILE-VAL-LYS
KeywordsMEMBRANE PROTEIN / STRUCTURE FROM CYANA 2.1
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 / 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 / torsion angle dynamics
AuthorsMcKay, R. / Wong, K. / Towle, K. / Fliegel, L.
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2019
Title: Diverse residues of intracellular loop 5 of the Na+/H+exchanger modulate proton sensing, expression, activity and targeting.
Authors: Wong, K.Y. / McKay, R. / Liu, Y. / Towle, K. / Elloumi, Y. / Li, X. / Quan, S. / Dutta, D. / Sykes, B.D. / Fliegel, L.
History
DepositionNov 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLY-LEU-THR-TRP-PHE-ILE-ASN-LYS-PHE-ARG-ILE-VAL-LYS


Theoretical massNumber of molelcules
Total (without water)1,6251
Polymers1,6251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Single synthetic peptide chain. No macromolecular assembly.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1500 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide GLY-LEU-THR-TRP-PHE-ILE-ASN-LYS-PHE-ARG-ILE-VAL-LYS


Mass: 1624.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P19634*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic11D Proton
121isotropic12D NOESY
131isotropic12D HSQC
141isotropic12D TOCSY

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Sample preparation

DetailsType: micelle / Contents: 5 mM peptide, 90% H2O/10% D2O
Details: 1663.03 g/mol 650 uL sample volume 5.4mg of peptide 440 mM SDS (i.e. 80x + 10%) 85.7mg of SDS delivered pH ~ 6 via paper dab check DSS 0.5 mM from stock
Label: SDS solvent / Solvent system: 90% H2O/10% D2O
SampleConc.: 5 mM / Component: peptide / Isotopic labeling: none
Sample conditionsDetails: 1663.03 g/mol 650 uL sample volume 5.4mg of peptide 440 mM SDS (i.e. 80x + 10%) 85.7mg of SDS delivered pH ~ 6 via paper dab check DSS 0.5 mM from stock
Ionic strength: 440 mM / Ionic strength err: 10 / Label: SDS / pH: 6 / PH err: 0.2 / Pressure: 960 mbar / Pressure err: 20 / Temperature: 300 K / Temperature err: 0.1

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz / Details: HCN probe

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ4.2Agilentcollection
NMRPipe8.9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 2 / Details: automatic
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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