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- PDB-6zbi: Ternary complex of Calmodulin bound to 2 molecules of NHE1 -

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Basic information

Entry
Database: PDB / ID: 6zbi
TitleTernary complex of Calmodulin bound to 2 molecules of NHE1
Components
  • Calmodulin-1
  • Sodium/hydrogen exchanger 1
KeywordsMETAL BINDING PROTEIN / Complex / NHE1 / Calmodulin / Signaling
Function / homology
Function and homology information


cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan 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 ...cation-transporting ATPase complex / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan 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 / response to acidic pH / intracellular sodium ion homeostasis / regulation of stress fiber assembly / cellular response to acidic pH / sodium ion import across plasma membrane / cardiac muscle cell contraction / positive regulation of mitochondrial membrane permeability / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / regulation of cardiac muscle contraction by calcium ion signaling / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / regulation of focal adhesion assembly / cellular response to antibiotic / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / positive regulation of cardiac muscle hypertrophy / cellular response to cold / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of the force of heart contraction / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / protein complex oligomerization / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / intercalated disc / DARPP-32 events / catalytic complex / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / monoatomic ion transport / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / cellular response to epinephrine stimulus / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / T-tubule / substantia nigra development / FCERI mediated Ca+2 mobilization / proton transmembrane transport / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / FCGR3A-mediated IL10 synthesis / calyx of Held
Similarity search - Function
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 / EF-hand / : / Recoverin; domain 1 ...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 / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / Sodium/hydrogen exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPrestel, A. / Kragelund, B.B. / Pedersen, E.S. / Pedersen, S.F. / Sjoegaard-Frich, L.M.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Danish National Research Foundation4181-00344 Denmark
Novo Nordisk FoundationSYNERGY Denmark
CitationJournal: Elife / Year: 2021
Title: Dynamic Na + /H + exchanger 1 (NHE1) - calmodulin complexes of varying stoichiometry and structure regulate Ca 2+ -dependent NHE1 activation.
Authors: Sjogaard-Frich, L.M. / Prestel, A. / Pedersen, E.S. / Severin, M. / Kristensen, K.K. / Olsen, J.G. / Kragelund, B.B. / Pedersen, S.F.
History
DepositionJun 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 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

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
B: Sodium/hydrogen exchanger 1
C: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6927
Polymers25,5313
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3150 Å2
ΔGint-29 kcal/mol
Surface area16290 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin-1


Mass: 16721.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Plasmid: pET5 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): codonPlus (DE3)-RP / References: UniProt: P0DP23
#2: Protein/peptide 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: 4405.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta2 pLysS / References: UniProt: P19634
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D 1H-13C NOESY aromatic
131isotropic13D 1H-15N NOESY
141isotropic13D 1H-15N NOESY 12C/14N filtered
151isotropic13D 1H-13C NOESY 12C/14N filtered
193isotropic13D 1H-13C NOESY
183isotropic13D 1H-15N NOESY
173isotropic13D 1H-13C NOESY 12C/14N filtered
163isotropic13D 1H-15N NOESY 12C/14N filtered
1101isotropic13D HNCO
1201isotropic13D HN(CA)CB
1191isotropic13D HN(CA)CO
1181isotropic13D C(CO)NH
1171isotropic13D (H)CCH-TOCSY
1161isotropic13D HBHA(CO)NH
1153isotropic13D (H)CCH-TOCSY
1143isotropic13D HBHA(CO)NH
1133isotropic13D HNCO
1123isotropic13D HN(CA)CB
1113isotropic13D CBCA(CO)NH
1213isotropic13D HN(CA)CO
1221isotropic12D 1H-13C HSQC
1231isotropic12D 1H-15N HSQC
1243isotropic12D 1H-13C HSQC
1253isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.15 mM Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 95% H2O/5% D2OD95% H2O/5% D2O
solution31 mM [U-99% 13C; U-99% 15N] Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 0.5 mM Calmodulin, 95% H2O/5% D2OE95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCalmodulin[U-99% 13C; U-99% 15N]1
1.15 mMSodium/Hydrogen exchanger 1 (NHE1, SLC9A1)natural abundance1
1 mMSodium/Hydrogen exchanger 1 (NHE1, SLC9A1)[U-99% 13C; U-99% 15N]3
0.5 mMCalmodulinnatural abundance3
Sample conditionsIonic strength: 120 mM / Ionic strength err: 10 / Label: NMR / pH: 7.5 / PH err: 0.2 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 310 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.44Schwieters, Kuszewski, Tjandra and Clorerefinement
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpin3.5Bruker Biospinprocessing
qMDDKazimierczuk, Orekhovprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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