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- PDB-6bv7: NMR structure of Sodium/Calcium Exchanger 1 (NCX1) Two-helix Bund... -

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Basic information

Entry
Database: PDB / ID: 6bv7
TitleNMR structure of Sodium/Calcium Exchanger 1 (NCX1) Two-helix Bundle (THB) domain
ComponentsSodium/calcium exchanger 1
KeywordsMEMBRANE PROTEIN / Two-helix Bundle
Function / homology
Function and homology information


Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Ion homeostasis / calcium:sodium antiporter activity / cell communication / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / ankyrin binding / positive regulation of the force of heart contraction ...Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Ion homeostasis / calcium:sodium antiporter activity / cell communication / sodium ion import across plasma membrane / intracellular sodium ion homeostasis / ankyrin binding / positive regulation of the force of heart contraction / calcium ion import across plasma membrane / sodium ion transmembrane transport / positive regulation of bone mineralization / response to muscle stretch / calcium ion transmembrane transport / sarcolemma / postsynapse / calmodulin binding / axon / calcium ion binding / nucleoplasm / plasma membrane
Similarity search - Function
Sodium/calcium exchanger, isoform 1 / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein ...Sodium/calcium exchanger, isoform 1 / Sodium/calcium exchanger protein / Sodium/calcium exchanger domain, C-terminal extension / C-terminal extension of sodium/calcium exchanger domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / NCX, central ion-binding domain superfamily / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / CalX-like domain superfamily / DnaJ domain
Similarity search - Domain/homology
Sodium/calcium exchanger 1
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodSOLUTION NMR / simulated annealing
AuthorsYuan, J. / Yuan, C. / Bruschweiler, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1715505 United States
CitationJournal: Biochemistry / Year: 2018
Title: The Intracellular Loop of the Na+/Ca2+Exchanger Contains an "Awareness Ribbon"-Shaped Two-Helix Bundle Domain.
Authors: Yuan, J. / Yuan, C. / Xie, M. / Yu, L. / Bruschweiler-Li, L. / Bruschweiler, R.
History
DepositionDec 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.6May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/calcium exchanger 1


Theoretical massNumber of molelcules
Total (without water)6,7891
Polymers6,7891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Sodium/calcium exchanger 1 / Na(+)/Ca(2+)-exchange protein 1 / Solute carrier family 8 member 1


Mass: 6788.544 Da / Num. of mol.: 1 / Fragment: residues 306-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: SLC8A1, NCX1 / Plasmid: pTBSG1 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23685

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
123isotropic12D 1H-13C HSQC
132isotropic23D HNCA
142isotropic23D HN(CO)CA
152isotropic23D HNCO
162isotropic23D HN(CA)CO
172isotropic23D HN(CA)CB
182isotropic23D HN(COCA)CB
193isotropic23D (H)CCH-TOCSY
1103isotropic23D (H)CCH-TOCSY
1112isotropic23D H(CO)NH-TOCSY
1122isotropic23D (H)CC(CO)NH-TOCSY
1133isotropic22D aromatic TROSY-HSQC
1144isotropic22D 1H-1H NOESY
1151isotropic23D HNHB
1164isotropic22D DQF-COSY
1175isotropic22D 10%-13C CT-HSQC
1182isotropic13D 15N-edited NOESY
1192isotropic13D 15N-edited CNH-NOESY
1203isotropic13D 13C-edited NOESY
1213isotropic13D 13C-edited CCH-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM [U-15N] NCX1_THB, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O15N_sample_H2O90% H2O/10% D2O
solution2300 uM [U-13C; U-15N] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 90% H2O/10% D2O15N_13C_sample_H2O90% H2O/10% D2O
solution3300 uM [U-13C; U-15N] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O15N_13C_sample_D2O100% D2O
solution4300 uM NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2Onon-label_sample_D2O100% D2O
solution5300 uM [U-10% 13C] NCX1 THB, 100 mM sodium chloride, 20 mM sodium phosphate, 100% D2O10%-13C_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMNCX1_THB[U-15N]1
100 mMsodium chloridenatural abundance1
20 mMsodium phosphatenatural abundance1
300 uMNCX1 THB[U-13C; U-15N]2
100 mMsodium chloridenatural abundance2
20 mMsodium phosphatenatural abundance2
300 uMNCX1 THB[U-13C; U-15N]3
100 mMsodium chloridenatural abundance3
20 mMsodium phosphatenatural abundance3
300 uMNCX1 THBnatural abundance4
100 mMsodium chloridenatural abundance4
20 mMsodium phosphatenatural abundance4
300 uMNCX1 THB[U-10% 13C]5
100 mMsodium chloridenatural abundance5
20 mMsodium phosphatenatural abundance5
Sample conditionsIonic strength: 100 mM NaCl, 20 mM Sodium Phosphate mM / Label: condition_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8501
Bruker AVANCE IIIBrukerAVANCE III7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
SparkyGoddarddata analysis
NMRViewJohnson, One Moon Scientificdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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