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- PDB-8bd2: Calcium-bound Calmodulin variant G113R -

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Basic information

Entry
Database: PDB / ID: 8bd2
TitleCalcium-bound Calmodulin variant G113R
ComponentsCalmodulin-3
KeywordsMETAL BINDING PROTEIN / Calmodulin Ca-binding protein Ca-signalling protein
Function / homology
Function and homology information


negative regulation of high voltage-gated calcium channel activity / negative regulation of calcium ion export across plasma membrane / 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 / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding ...negative regulation of high voltage-gated calcium channel activity / negative regulation of calcium ion export across plasma membrane / 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 / negative regulation of peptidyl-threonine phosphorylation / protein phosphatase activator activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / adenylate cyclase binding / catalytic complex / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / voltage-gated potassium channel complex / titin binding / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / regulation of heart rate / sarcomere / protein serine/threonine kinase activator activity / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / positive regulation of protein serine/threonine kinase activity / spindle microtubule / spindle pole / response to calcium ion / calcium-dependent protein binding / G2/M transition of mitotic cell cycle / myelin sheath / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / centrosome / calcium ion binding / protein kinase binding / protein-containing complex / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWimmer, R. / Holler, C.V. / Petersson, N.M. / Iwai, H. / Niemelae, M.A. / Brohus, M. / Overgaard, M.T.
Funding support Denmark, Finland, 5items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0053032 Denmark
Obel Family Foundation Denmark
Spar Nord Foundation Denmark
The Carlsberg Foundation Denmark
Instruct-ERIC Center (Helsinki)24613, 24616 Finland
CitationJournal: Cell Calcium / Year: 2023
Title: Allosteric changes in protein stability and dynamics as pathogenic mechanism for calmodulin variants not affecting Ca 2+ coordinating residues.
Authors: Holler, C.V. / Petersson, N.M. / Brohus, M. / Niemela, M.A. / Iversen, E.D. / Overgaard, M.T. / Iwai, H. / Wimmer, R.
History
DepositionOct 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9023
Polymers16,8211
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area170 Å2
ΔGint-25 kcal/mol
Surface area5000 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Calmodulin-3 /


Mass: 16821.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Only the C-lobe of Calmodulin (from Ser81 to Lys 148) was isotopically labelled, thus resonance assignment and structure were only determined for the C-lobe.
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM3, CALML2, CAM3, CAMC, CAMIII / Production host: Escherichia coli (E. coli) / References: UniProt: P0DP25
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CO
181isotropic13D CBCA(CO)NH
171isotropic13D CBCANH
161isotropic13D HNCA
1111isotropic13D HBHA(CO)NH
1101isotropic12D-CACO
191isotropic12D-(HB)CB(CGCD)HD
1141isotropic12D-(HB)CB(CGCDCE)HE
1131isotropic13D 1H-13C NOESY aliphatic
1121isotropic13D 1H-13C NOESY aromatic
1151isotropic13D 1H-15N NOESY
1171isotropic13D (H)CC(CO)NH
1161isotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 100 mM potassium chloride, 5 mM calcium chloride, 2 mM sodium azide, 20 mM HEPES, 0.1 mM 2,2,3,3-tetradeutero TSP-d4, 1 mM (Ser81-Lys148-U-15N,13C) Calmodulin G113R, 95% H2O/5% D2O
Details: The sample contained native full-length Calmodulin (Ala 1 - Lys 148), whereof only Ser 81 - Lys 148 were isotopically labelled.
Label: (Ser81-Lys148-U-15N,13C)-Ca/CaM-G113R / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMpotassium chloridenatural abundance1
5 mMcalcium chloridenatural abundance1
2 mMsodium azidenatural abundance1
20 mMHEPESnatural abundance1
0.1 mMTSP-d42,2,3,3-tetradeutero1
1 mMCalmodulin G113R(Ser81-Lys148-U-15N,13C)1
Sample conditionsIonic strength: 127 mM / Label: condition_1 / pH: 6.69 / Pressure: 1 atm / Temperature: 298.1 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz / Details: CPP-TCI probe

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Processing

NMR software
NameVersionDeveloperClassification
YASARA20.12.24Elmar Krieger YASARA Biosciencerefinement
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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