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- PDB-2fwu: Second Ca2+ binding domain of the Na,Ca-exchanger (NCX1) -

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Basic information

Entry
Database: PDB / ID: 2fwu
TitleSecond Ca2+ binding domain of the Na,Ca-exchanger (NCX1)
ComponentsSodium/calcium exchanger 1
KeywordsMETAL TRANSPORT REGULATOR / beta-sandwich / greek key / beta-bulge / Ca2+ binding
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 / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / 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 / intracellular sodium ion homeostasis / sodium ion import across plasma membrane / 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 / CalX-beta domain / 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, isoform 1 / CalX-beta domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium/calcium exchanger 1
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHilge, M. / Vuister, G.W. / Aelen, J.
CitationJournal: Mol.Cell / Year: 2006
Title: Ca(2+) regulation in the na(+)/ca(2+) exchanger involves two markedly different ca(2+) sensors
Authors: Hilge, M. / Aelen, J. / Vuister, G.W.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium/calcium exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8993
Polymers17,8191
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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


Mass: 17818.832 Da / Num. of mol.: 1 / Fragment: CBD2, Ca2+ binding domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Species: Canis lupus / Strain: familiaris / Gene: NCX1 / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P23685
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C separated aliphatic NOESY
1213D 13C separated aromatic NOESY
1313D 15N-separated NOESY

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Sample preparation

DetailsContents: 0.5-1.0mM 13C, 15N labeled CBD2 sample in 20mM HEPES (pH 7.0), 20mM beta-Mercaptoethanol buffer
Solvent system: 95% ddH2O, 5% D2O
Sample conditionsIonic strength: 20mM HEPES (sodium salt) / pH: 7.0 / Pressure: ambient / Temperature: 306 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, F.processing
XEASY1.3.13Bartels, C.data analysis
CYANA2Guentert, P.structure solution
X-PLORNIH version 2.9.7Clore, G.M.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on 2394 NOE-derived distance constraints, 185 dihedral angle restraints (talos), 8 distance constraints to the 2 Ca2+ ions
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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