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- PDB-7jgi: NMR structure of the cNTnC-cTnI chimera bound to A7 -

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Basic information

Entry
Database: PDB / ID: 7jgi
TitleNMR structure of the cNTnC-cTnI chimera bound to A7
ComponentsTroponin C, slow skeletal and cardiac muscles,Troponin I, cardiac muscle chimera
KeywordsMETAL BINDING PROTEIN / cardiac troponin / calcium binding protein / EF hand / calcium modulator
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / troponin C binding / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / regulation of smooth muscle contraction / troponin complex ...regulation of systemic arterial blood pressure by ischemic conditions / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / troponin C binding / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / regulation of smooth muscle contraction / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / negative regulation of ATP-dependent activity / Striated Muscle Contraction / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / ventricular cardiac muscle tissue morphogenesis / myosin II complex / heart contraction / troponin I binding / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / cardiac muscle contraction / Ion homeostasis / 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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...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
Chem-V8Y / Troponin I, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCai, F. / Robertson, I.M. / Kampourakis, T. / Klein, B.A. / Sykes, B.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other privateB.D.S., G-14-0005884 Canada
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: The Role of Electrostatics in the Mechanism of Cardiac Thin Filament Based Sensitizers.
Authors: Cai, F. / Robertson, I.M. / Kampourakis, T. / Klein, B.A. / Sykes, B.D.
History
DepositionJul 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 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 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5963
Polymers14,1861
Non-polymers4102
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area8380 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 14186.127 Da / Num. of mol.: 1 / Mutation: 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63316, UniProt: P19429
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-V8Y / 7-{[(5-chloronaphthalen-1-yl)sulfonyl]amino}heptanoic acid


Mass: 369.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20ClNO4S / 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
122isotropic12D 1H-13C HSQC
132isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-15N] cChimera_protein, 100 mM potassium chloride, 10 mM imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 1.5 mM A7, 1 % [U-99% 2H] DMSO, 95% H2O/5% D2O15N_chimera95% H2O/5% D2O
solution20.5 mM [U-15N] cChimera_protein, 100 mM potassium chloride, 10 mM imidazole, 10 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 0.7 mM A7, 1 mM [U-99% 2H] DMSO, 100% D2O13C_15N_chimera100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMcChimera_protein[U-15N]1
100 mMpotassium chloridenatural abundance1
10 mMimidazolenatural abundance1
10 mMcalcium chloridenatural abundance1
0.25 mMDSS[U-99% 2H]1
1.5 mMA7natural abundance1
1 %DMSO[U-99% 2H]1
0.5 mMcChimera_protein[U-15N]2
100 mMpotassium chloridenatural abundance2
10 mMimidazolenatural abundance2
10 mMcalcium chloridenatural abundance2
0.25 mMDSS[U-99% 2H]2
0.7 mMA7natural abundance2
1 mMDMSO[U-99% 2H]2
Sample conditionsIonic strength: NA Not defined / Label: NMR_sample / pH: 6.7 / PH err: 0.1 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
VnmrJVarianrefinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJJohnson, One Moon Scientificpeak picking
NMRViewJJohnson, One Moon Scientificchemical shift assignment
ARIALinge, O'Donoghue and Nilgesdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 10

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