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- PDB-2m7x: Structural and Functional Analysis of Transmembrane Segment IV of... -

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Basic information

Entry
Database: PDB / ID: 2m7x
TitleStructural and Functional Analysis of Transmembrane Segment IV of the Salt Tolerance Protein Sod2
ComponentsNa(+)/H(+) antiporter
KeywordsMEMBRANE PROTEIN / sod2 / transmembrane
Function / homology
Function and homology information


plasma membrane of cell tip / intracellular pH reduction / prospore membrane / sodium:proton antiporter activity / perinuclear endoplasmic reticulum membrane / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / nuclear outer membrane-endoplasmic reticulum membrane network / plasma membrane => GO:0005886 ...plasma membrane of cell tip / intracellular pH reduction / prospore membrane / sodium:proton antiporter activity / perinuclear endoplasmic reticulum membrane / sodium ion export across plasma membrane / intracellular potassium ion homeostasis / intracellular sodium ion homeostasis / nuclear outer membrane-endoplasmic reticulum membrane network / plasma membrane => GO:0005886 / sodium ion transmembrane transport / proton transmembrane transport / plasma membrane
Similarity search - Function
Na+/H+ antiporter, fungi / Cation/H+ exchanger / Sodium/hydrogen exchanger family
Similarity search - Domain/homology
Na(+)/H(+) antiporter
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsUllah, A. / Kemp, G. / Lee, B. / Alves, C. / Young, H. / Sykes, B.D. / Fliegel, L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural and Functional Analysis of Transmembrane Segment IV of the Salt Tolerance Protein Sod2.
Authors: Ullah, A. / Kemp, G. / Lee, B. / Alves, C. / Young, H. / Sykes, B.D. / Fliegel, L.
History
DepositionMay 2, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Sep 11, 2013Group: Database references
Revision 1.3Oct 12, 2016Group: Structure summary
Revision 1.4Jun 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 1.5May 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+)/H(+) antiporter


Theoretical massNumber of molelcules
Total (without water)3,9931
Polymers3,9931
Non-polymers00
Water0
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/peptide Na(+)/H(+) antiporter


Mass: 3992.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Description: Maltose Binding Protein fusion / Gene: sod2, SPAC977.10 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P36606

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: NMR solution model of transmembrane segment IV Sod2 in organic solvent
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY-HSQC
1313D 1H-15N TOCSY-HSQC
1413D HNHA

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Sample preparation

DetailsContents: 0.2-0.7 mM [U-99% 15N] Sod2, 50 v/v CDCl3, 50 v/v 2-propanol, CDCl3/2-propanol
Solvent system: CDCl3/2-propanol
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-99% 15N]0.2-0.71
50 v/vCDCl3-21
50 v/v2-propanol-31
Sample conditionsIonic strength: not measured / Pressure: ambient / Temperature: 303.15 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJJohnson, One Moon Scientificpeak picking
NMRViewJJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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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