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- PDB-2mdf: NMR structure of a two-transmembrane segment TM VI-VII of NHE1 -

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Basic information

Entry
Database: PDB / ID: 2mdf
TitleNMR structure of a two-transmembrane segment TM VI-VII of NHE1
ComponentsSodium/hydrogen exchanger 1
KeywordsPROTON TRANSPORT / NHE1 / Na+/H+ exchanger / transmembrane
Function / homology
Function and homology information


cation-transporting ATPase complex / : / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity ...cation-transporting ATPase complex / : / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity / maintenance of cell polarity / regulation of pH / sodium ion export across plasma membrane / positive regulation of calcineurin-NFAT signaling cascade / cardiac muscle cell differentiation / protein phosphatase 2B binding / cellular response to acidic pH / intracellular sodium ion homeostasis / regulation of stress fiber assembly / sodium ion import across plasma membrane / cardiac muscle cell contraction / response to acidic pH / positive regulation of mitochondrial membrane permeability / regulation of cardiac muscle contraction by calcium ion signaling / cellular response to antibiotic / regulation of focal adhesion assembly / cellular response to cold / positive regulation of cardiac muscle hypertrophy / positive regulation of the force of heart contraction / protein complex oligomerization / : / intercalated disc / monoatomic ion transport / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / cellular response to epinephrine stimulus / potassium ion transmembrane transport / T-tubule / proton transmembrane transport / regulation of intracellular pH / stem cell differentiation / phospholipid binding / cellular response to insulin stimulus / cellular response to mechanical stimulus / calcium-dependent protein binding / cell migration / lamellipodium / positive regulation of cell growth / protein-macromolecule adaptor activity / basolateral plasma membrane / molecular adaptor activity / cellular response to hypoxia / calmodulin binding / apical plasma membrane / positive regulation of apoptotic process / membrane raft / 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
Helix Hairpins - #1330 / 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, transmembrane / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Sodium/hydrogen exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsLee, B.L. / Sykes, B.D. / Alves, C. / Fliegel, L.
CitationJournal: Biochemistry / Year: 2014
Title: Structural and Functional Analysis of the Transmembrane Segment Pair VI and VII of the NHE1 Isoform of the Na(+)/H(+) Exchanger.
Authors: Alves, C. / Lee, B.L. / Sykes, B.D. / Fliegel, L.
History
DepositionSep 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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 / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/hydrogen exchanger 1


Theoretical massNumber of molelcules
Total (without water)6,2571
Polymers6,2571
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)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sodium/hydrogen exchanger 1 / APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute ...APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1


Mass: 6257.360 Da / Num. of mol.: 1
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): XL1 Blue / References: UniProt: P19634

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
1313D 1H-15N TOCSY
1412D DQF-COSY
1512D 1H-1H TOCSY
1612D 1H-1H NOESY
1722D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11-2 mM [U-15N] entity, 5 % [U-2H] D2O, 0.25 mM [1,1,2,2,3,3-2H6] DSS, 95 % H2O, 75-150 mM [U-2H] dodecylphosphocholine, 95% H2O/5% D2O95% H2O/5% D2O
21-2 mM [U-15N] entity, 100 % [U-2H] D2O, 0.25 mM [1,1,2,2,3,3-2H6] DSS, 75-150 mM [U-2H] dodecylphosphocholine, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-15N]1-21
5 %D2O-2[U-2H]1
0.25 mMDSS-3[1,1,2,2,3,3-2H6]1
95 %H2O-41
mMdodecylphosphocholine-5[U-2H]75-1501
mMentity-6[U-15N]1-22
100 %D2O-7[U-2H]2
0.25 mMDSS-8[1,1,2,2,3,3-2H6]2
mMdodecylphosphocholine-9[U-2H]75-1502
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1748 / NOE intraresidue total count: 452 / NOE long range total count: 31 / NOE medium range total count: 389 / NOE sequential total count: 392 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 35 / Protein psi angle constraints total count: 35
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

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