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- PDB-2lt9: The solution structure of Ca2+ binding domain 2B of the third iso... -

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Basic information

Entry
Database: PDB / ID: 2lt9
TitleThe solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger
ComponentsProtein Slc8a3
KeywordsMETAL BINDING PROTEIN / NCX / NCX3 / NaCa exchanger / CBD / CBD2 / calcium binding domain 2
Function / homology
Function and homology information


calcium:monoatomic cation antiporter activity / monoatomic ion antiporter activity involved in regulation of postsynaptic membrane potential / calcium ion export across plasma membrane / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / : / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / : / regulation of skeletal muscle contraction / mitochondrial calcium ion transmembrane transport ...calcium:monoatomic cation antiporter activity / monoatomic ion antiporter activity involved in regulation of postsynaptic membrane potential / calcium ion export across plasma membrane / calcium:monoatomic cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration / : / Reduction of cytosolic Ca++ levels / Sodium/Calcium exchangers / : / regulation of skeletal muscle contraction / mitochondrial calcium ion transmembrane transport / mitochondrial calcium ion homeostasis / calcium:sodium antiporter activity / metal ion transport / telencephalon development / cell communication / Ion homeostasis / negative regulation of protein serine/threonine kinase activity / calcium ion transport into cytosol / sodium ion transport / oligodendrocyte differentiation / plasma membrane => GO:0005886 / modulation of excitatory postsynaptic potential / sarcoplasm / calcium ion import across plasma membrane / sodium ion transmembrane transport / hematopoietic progenitor cell differentiation / axon terminus / cellular response to cAMP / myelination / learning / cell projection / calcium ion transmembrane transport / long-term synaptic potentiation / synapse organization / neuromuscular junction / sarcolemma / memory / intracellular calcium ion homeostasis / cellular response to hypoxia / perikaryon / microtubule / mitochondrial outer membrane / dendritic spine / postsynaptic density / learning or memory / calmodulin binding / axon / neuronal cell body / synapse / dendrite / endoplasmic reticulum membrane / perinuclear region of cytoplasm / mitochondrion / metal ion binding / plasma membrane
Similarity search - Function
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 / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / CalX-like domain superfamily ...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 / Sodium/calcium exchanger membrane region / Sodium/calcium exchanger protein / CalX-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sodium/calcium exchanger 3 / Sodium/calcium exchanger 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsBreukels, V. / Touw, W.G. / Vuister, G.W.
CitationJournal: J.Biomol.Nmr / Year: 2012
Title: NMR structure note: solution structure of Ca(2+) binding domain 2B of the third isoform of the Na(+)/Ca (2+) exchanger.
Authors: Breukels, V. / Touw, W.G. / Vuister, G.W.
History
DepositionMay 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Slc8a3


Theoretical massNumber of molelcules
Total (without water)17,9001
Polymers17,9001
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)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein Slc8a3 / Slc8a3 protein / Slc8a3 protein


Mass: 17900.031 Da / Num. of mol.: 1 / Fragment: calcium binding domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc8a3 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7TS90, UniProt: S4R2P9*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: The solution structure of calcium binding domain 2B of NCX3 is solved in excess of 10 mM CaCl2. However, Ca ions are not modeled in the structure, because resonances of crucial coordinating ...Details: The solution structure of calcium binding domain 2B of NCX3 is solved in excess of 10 mM CaCl2. However, Ca ions are not modeled in the structure, because resonances of crucial coordinating residues are lacking: res 605 to 610 and 665 to 669.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D HNHA
1822D 1H-15N IPAP HSQC
1932D 1H-13C IPAP HSQC
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic
11213D 1H-15N NOESY
11313D C(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] protein, 20 mM HEPES, 20 mM beta-mercaptoethanol, 10 mM CaCl2, 95% H2O/5% D2O95% H2O/5% D2O
20.5 mM [U-100% 15N] protein, 20 mM HEPES, 20 mM beta-mercaptoethanol, 10 mM CaCl2, 8 mg/mL Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM [U-100% 15N] protein, 20 mM HEPES, 20 mM beta-mercaptoethanol, 10 mM CaCl2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-100% 13C; U-100% 15N]1
20 mMHEPES-21
20 mMbeta-mercaptoethanol-31
10 mMCaCl2-41
0.5 mMentity-5[U-100% 15N]2
20 mMHEPES-62
20 mMbeta-mercaptoethanol-72
10 mMCaCl2-82
8 mg/mLPf1 phage-92
0.5 mMentity-10[U-100% 15N]3
20 mMHEPES-113
20 mMbeta-mercaptoethanol-123
10 mMCaCl2-133
Sample conditionsIonic strength: 20 / 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
CCPN_Analysis2.2.2CCPNchemical shift assignment
CCPN_Analysis2.2.2CCPNpeak picking
NMRPipe2007Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw2007Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
YASARA11.9.18E. Krieger, Koraimann G, Vriend Grefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE SOLUTION STRUCTURE OF CALCIUM BINDING DOMAIN 2B OF NCX3 IS SOLVED IN EXCESS OF 10 MM CACL2. HOWEVER, CA IONS ARE NOT MODELED IN THE STRUCTURE, BECAUSE RESONANCES OF CRUCIAL COORDINATING ...Details: THE SOLUTION STRUCTURE OF CALCIUM BINDING DOMAIN 2B OF NCX3 IS SOLVED IN EXCESS OF 10 MM CACL2. HOWEVER, CA IONS ARE NOT MODELED IN THE STRUCTURE, BECAUSE RESONANCES OF CRUCIAL COORDINATING RESIDUES ARE LACKING: RES 605 TO 610 AND 665 TO 669. THE REFINEMENT PROTOCOL IN EXPLICIT WATER, INCLUDING DISTANCE AND DIHEDRAL RESTRAINTS. THE RDC RESTRAINTS WERE NOT INCLUDED IN THE REFINEMENT.
NMR constraintsNOE constraints total: 2901 / NOE long range total count: 1289 / NOE medium range total count: 279 / Protein phi angle constraints total count: 93 / Protein psi angle constraints total count: 93
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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