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- PDB-2kfx: Structure of the N-terminal domain of human cardiac troponin C bo... -

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Basic information

Entry
Database: PDB / ID: 2kfx
TitleStructure of the N-terminal domain of human cardiac troponin C bound to calcium ion and to the inhibitor W7
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsMETAL BINDING PROTEIN / calcium regulation / striated muscle / cardiac / troponin / W7 / cardiotonic drugs / Acetylation / Calcium / Cardiomyopathy / Disease mutation / Muscle protein / Polymorphism
Function / homology
Function and homology information


diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / muscle filament sliding ...diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction / muscle filament sliding / response to metal ion / ventricular cardiac muscle tissue morphogenesis / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / sarcomere / calcium-dependent protein binding / actin filament binding / calcium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
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-WW7 / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsHoffman, R.M.B. / Sykes, B.D.
Citation
Journal: Biochemistry / Year: 2009
Title: Structure of the inhibitor W7 bound to the regulatory domain of cardiac troponin C.
Authors: Hoffman, R.M. / Sykes, B.D.
#1: Journal: Biochemistry / Year: 1999
Title: Binding of cardiac troponin-I147-163 induces a structural opening in human cardiac troponin-C.
Authors: Li, M.X. / Spyracopoulos, L. / Sykes, B.D.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Structure of the regulatory N-domain of human cardiac troponin C in complex with human cardiac troponin I147-163 and bepridil.
Authors: Wang, X. / Li, M.X. / Sykes, B.D.
History
DepositionFeb 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
T: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4193
Polymers10,0381
Non-polymers3812
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Troponin C, slow skeletal and cardiac muscles / TN-C


Mass: 10038.173 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 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P63316
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-WW7 / N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE


Mass: 340.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21ClN2O2S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the N-terminal domain of human cardiac troponin C bound to the inhibitor W7 determined through isotopically edited and filtered transferred NOEs. This is based on the initial ...Details: Structure of the N-terminal domain of human cardiac troponin C bound to the inhibitor W7 determined through isotopically edited and filtered transferred NOEs. This is based on the initial coordinates of 1LXF, the intraprotein conformational restraints of 1MXL, and target geometries for a calcium-binding loop. The amine moiety of W7 is charged in this structure determination.
NMR experimentType: 3D-{1H,12C}-filtered-{1H,13C}-edited NOESY

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Sample preparation

DetailsContents: 0.8 mM [U-99% 13C; U-99% 15N] cNTnC, 4.9 mM CALCIUM ION, 0.8 mM N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE, 10 mM imidazole, 83 mM [U-99% 2H] DSS, 100% D2O
Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMcNTnC[U-99% 13C; U-99% 15N]1
4.9 mMCALCIUM ION1
0.8 mMN-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE1
10 mMimidazole1
83 mMDSS[U-99% 2H]1
Sample conditionspH: 6.75 / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
VnmrJVarianprocessing
Xplor-NIH2.21Schwieters, C. et al.refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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