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- PDB-2l53: Solution NMR Structure of apo-calmodulin in complex with the IQ m... -

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Basic information

Entry
Database: PDB / ID: 2l53
TitleSolution NMR Structure of apo-calmodulin in complex with the IQ motif of Human Cardiac Sodium Channel NaV1.5
Components
  • Calmodulin
  • Voltage-gated sodium channel type V alpha isoform b variant
KeywordsCA-BINDING PROTEIN/PROTON TRANSPORT / calmodulin / IQ motif / complex / Ca-Binding Protein / CA-BINDING PROTEIN-PROTON TRANSPORT complex
Function / homology
Function and homology information


voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication / negative regulation of calcium ion transmembrane transporter activity / membrane depolarization during SA node cell action potential ...voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / SA node cell action potential / AV node cell to bundle of His cell communication / negative regulation of calcium ion transmembrane transporter activity / membrane depolarization during SA node cell action potential / response to denervation involved in regulation of muscle adaptation / membrane depolarization during atrial cardiac muscle cell action potential / cardiac ventricle development / regulation of atrial cardiac muscle cell membrane repolarization / regulation of ventricular cardiac muscle cell membrane depolarization / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / brainstem development / membrane depolarization during AV node cell action potential / positive regulation of action potential / membrane depolarization during bundle of His cell action potential / atrial cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction system development / telencephalon development / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of sodium ion transmembrane transport / regulation of atrial cardiac muscle cell membrane depolarization / : / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / establishment of protein localization to mitochondrial membrane / positive regulation of sodium ion transport / negative regulation of peptidyl-threonine phosphorylation / type 3 metabotropic glutamate receptor binding / ventricular cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / voltage-gated sodium channel complex / regulation of cardiac muscle cell contraction / Interaction between L1 and Ankyrins / ankyrin binding / voltage-gated sodium channel activity / positive regulation of DNA binding / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / positive regulation of peptidyl-threonine phosphorylation / nitric-oxide synthase binding / negative regulation of calcium ion export across plasma membrane / sodium ion transport / regulation of synaptic vesicle exocytosis / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / fibroblast growth factor binding / calcineurin-mediated signaling / odontogenesis of dentin-containing tooth / regulation of heart rate by cardiac conduction / regulation of synaptic vesicle endocytosis / positive regulation of protein autophosphorylation / protein phosphatase activator activity / adenylate cyclase binding / membrane depolarization / intercalated disc / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / positive regulation of protein serine/threonine kinase activity / lateral plasma membrane / phosphatidylinositol 3-kinase binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / cardiac muscle contraction / enzyme regulator activity / regulation of calcium-mediated signaling / titin binding / voltage-gated potassium channel complex / T-tubule / sperm midpiece / substantia nigra development / calcium channel complex / sodium ion transmembrane transport / calyx of Held / nitric-oxide synthase regulator activity / response to amphetamine / positive regulation of nitric-oxide synthase activity / cerebellum development / adenylate cyclase activator activity / regulation of heart rate / cellular response to calcium ion / protein serine/threonine kinase activator activity / sarcomere / positive regulation of epithelial cell proliferation
Similarity search - Function
Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily ...Voltage gated sodium channel, alpha-5 subunit / Voltage-gated Na+ ion channel, cytoplasmic domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Sodium ion transport-associated / Voltage-gated sodium channel alpha subunit, inactivation gate / Sodium ion transport-associated / SCN5A-like, C-terminal IQ motif / Voltage gated sodium channel, alpha subunit / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / : / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Calmodulin-2 / Calmodulin-3 / Sodium channel protein type 5 subunit alpha / Sodium channel protein type 5 subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsChagot, B. / Chazin, W.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Solution NMR Structure of Apo-Calmodulin in Complex with the IQ Motif of Human Cardiac Sodium Channel NaV1.5.
Authors: Chagot, B. / Chazin, W.J.
History
DepositionOct 24, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calmodulin
B: Voltage-gated sodium channel type V alpha isoform b variant


Theoretical massNumber of molelcules
Total (without water)20,2502
Polymers20,2502
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Calmodulin / CaM


Mass: 16721.350 Da / Num. of mol.: 1 / Fragment: calmodulin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP24*PLUS
#2: Protein/peptide Voltage-gated sodium channel type V alpha isoform b variant


Mass: 3529.107 Da / Num. of mol.: 1 / Fragment: Human Cardiac Sodium Channel NaV1.5 IQ motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q59H93, UniProt: Q14524*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-1H NOESY
1222D 1H-1H COSY
1312D 1H-15N HSQC
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D HNCO
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11122D 1H-1H TOCSY
11213D (H)CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] calmodulin, 1 mM [U-99% 13C; U-99% 15N] entity_2-2, 95% H2O/5% D2O95% H2O/5% D2O
21 mM entity_1-3, 1 mM entity_2-4, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-99% 13C; U-99% 15N]1
1 mMentity_2-2[U-99% 13C; U-99% 15N]1
1 mMentity_1-32
1 mMentity_2-42
Sample conditionsIonic strength: 100 / pH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
Amber10Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
TopSpinBruker Biospincollection
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: restrained molecular dynamic
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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