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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


positive regulation of mitochondrial membrane permeability / regulation of the force of heart contraction by cardiac conduction / Sodium/Proton exchangers / Hyaluronan degradation / cation-transporting ATPase complex / cellular response to electrical stimulus / regulation of cardiac muscle cell membrane potential / potassium:proton antiporter activity / regulation of pH / positive regulation of action potential ...positive regulation of mitochondrial membrane permeability / regulation of the force of heart contraction by cardiac conduction / Sodium/Proton exchangers / Hyaluronan degradation / cation-transporting ATPase complex / cellular response to electrical stimulus / regulation of cardiac muscle cell membrane potential / potassium:proton antiporter activity / regulation of pH / positive regulation of action potential / hyaluronan catabolic process / maintenance of cell polarity / sodium:proton antiporter activity / positive regulation of calcineurin-NFAT signaling cascade / cellular response to cold / sodium ion export across plasma membrane / protein phosphatase 2B binding / regulation of stress fiber assembly / intracellular sodium ion homeostasis / response to acidic pH / sodium ion import across plasma membrane / CaM pathway / regulation of focal adhesion assembly / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of cardiac muscle contraction by calcium ion signaling / cellular response to antibiotic / cardiac muscle cell contraction / 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 / PKA activation / CaMK IV-mediated phosphorylation of CREB / positive regulation of cardiac muscle hypertrophy / CASP4 inflammasome assembly / Glycogen breakdown (glycogenolysis) / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / positive regulation of the force of heart contraction / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / response to muscle stretch / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / regulation of cell communication by electrical coupling involved in cardiac conduction / protein complex oligomerization / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / intercalated disc / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / presynaptic cytosol / cellular response to acidic pH / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / regulation of heart rate / Protein methylation / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol-4,5-bisphosphate binding / voltage-gated potassium channel complex / cellular response to epinephrine stimulus / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / proton transmembrane transport / FCGR3A-mediated IL10 synthesis / potassium ion transmembrane transport / T-tubule / protein serine/threonine kinase activator activity / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / 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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