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- PDB-5wcl: NMR structure of the N-domain of troponin C bound to switch regio... -

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Basic information

Entry
Database: PDB / ID: 5wcl
TitleNMR structure of the N-domain of troponin C bound to switch region of troponin I and 3-methyldiphenylamine (solvent exposed mode)
ComponentsTroponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle
KeywordsMETAL BINDING PROTEIN / cardiac troponin / calcium binding protein / EF hand / calcium sensitizer
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of muscle contraction ...regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of muscle contraction / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / Striated Muscle Contraction / muscle filament sliding / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / ventricular cardiac muscle tissue morphogenesis / heart contraction / troponin I binding / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / Ion homeostasis / cardiac muscle contraction / sarcomere / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / actin binding / heart development / protein domain specific binding / calcium ion binding / protein kinase binding / protein homodimerization activity / cytosol
Similarity search - Function
Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / : / EF-hand domain pair / EF-hand, calcium binding motif ...Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / : / 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
3-methyl-N-phenylaniline / Troponin I, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsCai, F. / Hwang, P.M. / Sykes, B.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Heart and Stroke Foundation of CanadaB.D.S., G-14-0005884 Canada
CitationJournal: J. Mol. Cell. Cardiol. / Year: 2016
Title: Structures reveal details of small molecule binding to cardiac troponin.
Authors: Cai, F. / Li, M.X. / Pineda-Sanabria, S.E. / Gelozia, S. / Lindert, S. / West, F. / Sykes, B.D. / Hwang, P.M.
History
DepositionJun 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Troponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6792
Polymers13,4951
Non-polymers1831
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 80structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Troponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle / TN-C / Cardiac troponin I


Mass: 13495.394 Da / Num. of mol.: 1 / Mutation: C35S, C84S,C35S, C84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC, TNNI3, TNNC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63316, UniProt: P19429
#2: Chemical ChemComp-9XG / 3-methyl-N-phenylaniline


Mass: 183.249 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H13N

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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
121isotropic13D HNHB
131isotropic13D 1H-15N NOESY
142isotropic13D CBCA(CO)NH
152isotropic13D HN(CA)CB
162isotropic13D HNCO
172isotropic13D HN(CA)CO
182isotropic13D C(CO)NH
192isotropic13D H(CCO)NH
1104isotropic12D 1H-13C HSQC
1113isotropic22D 1H-13C HSQC
1123isotropic23D 1H-13C NOESY
1133isotropic23D 1H-13C NOESY aromatic
1143isotropic22D 13C,15N-double-filtered NOESY
1153isotropic23D 13C-filtered NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.25 mM [U-15N] cChimera_protein, 100 mM potassium chloride, 10 mM imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 0.5 mM 3-methyldiphenylamine, 95% H2O/5% D2O15N_chimera95% H2O/5% D2O
solution20.5 mM [U-13C; U-15N] cChimera_protein, 100 mM potassium chloride, 10 mM imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 0.8 mM 3-methyldiphenylamine, 95% H2O/5% D2O13C_N15_chimera95% H2O/5% D2O
solution30.5 mM [U-13C; U-15N] cChimera_protein, 100 mM potassium chloride, 10 mM [U-99% 2H] imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 0.8 mM 3-methyldiphenylamine, 100% D2O13C_N15_chimera_D2O100% D2O
solution40.5 mM [U-10% 13C; U-100% 15N] cChimera_protein, 100 mM potassium chloride, 10 mM imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 0.8 mM 3-methyldiphenylamine, 95% H2O/5% D2O10%13C_N15_chimera95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMcChimera_protein[U-15N]1
100 mMpotassium chloridenatural abundance1
10 mMimidazolenatural abundance1
10 mMcalcium chloridenatural abundance1
0.25 mMDSS[U-99% 2H]1
0.5 mM3-methyldiphenylaminenatural abundance1
0.5 mMcChimera_protein[U-13C; U-15N]2
100 mMpotassium chloridenatural abundance2
10 mMimidazolenatural abundance2
10 mMcalcium chloridenatural abundance2
0.25 mMDSS[U-99% 2H]2
0.8 mM3-methyldiphenylaminenatural abundance2
0.5 mMcChimera_protein[U-13C; U-15N]3
100 mMpotassium chloridenatural abundance3
10 mMimidazole[U-99% 2H]3
10 mMcalcium chloridenatural abundance3
0.25 mMDSS[U-99% 2H]3
0.8 mM3-methyldiphenylaminenatural abundance3
0.5 mMcChimera_protein[U-10% 13C; U-100% 15N]4
100 mMpotassium chloridenatural abundance4
10 mMimidazolenatural abundance4
10 mMcalcium chloridenatural abundance4
0.25 mMDSS[U-99% 2H]4
0.8 mM3-methyldiphenylaminenatural abundance4
Sample conditionsIonic strength: NA Not defined / Label: NMR_sample / pH: 6.8 / Pressure: ambient atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJJohnson, One Moon Scientificpeak picking
NMRViewJJohnson, One Moon Scientificchemical shift assignment
ARIA2Linge, O'Donoghue and Nilgesstructure calculation
ARIA2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 6
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 8

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