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- PDB-2krd: Solution Structure of the Regulatory Domain of Human Cardiac Trop... -

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Basic information

Entry
Database: PDB / ID: 2krd
TitleSolution Structure of the Regulatory Domain of Human Cardiac Troponin C in Complex with the Switch Region of cardiac Troponin I and W7
Components
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
KeywordsSTRUCTURAL PROTEIN / cardiac troponin C / regulatory domain / troponin I / switch region / W7 / Acetylation / Calcium / Cardiomyopathy / Disease mutation / Muscle protein / Polymorphism / Actin-binding / Phosphoprotein
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of smooth muscle contraction ...regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of smooth muscle contraction / 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 / heart contraction / troponin I binding / skeletal muscle contraction / vasculogenesis / calcium channel inhibitor activity / cardiac muscle contraction / Ion homeostasis / sarcomere / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / heart development / actin binding / 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
Chem-WW7 / Troponin I, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsOleszczuk, M. / Robertson, I.M. / Li, M.X. / Sykes, B.D.
CitationJournal: J.MOL.CELL.CARDIOL. / Year: 2010
Title: Solution structure of the regulatory domain of human cardiac troponin C in complex with the switch region of cardiac troponin I and W7: the basis of W7 as an inhibitor of cardiac muscle contraction.
Authors: Oleszczuk, M. / Robertson, I.M. / Li, M.X. / Sykes, B.D.
History
DepositionDec 16, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,2574
Polymers11,8762
Non-polymers3812
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 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 10070.304 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: P63316
#2: Protein/peptide Troponin I, cardiac muscle / Cardiac troponin I


Mass: 1806.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P19429
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1352D DQF-COSY
1423D CBCA(CO)NH
1523D C(CO)NH
1623D HN(CA)CB
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1952D 1H-1H NOESY
11032D CNfilnoesy
11132D CNfiltocsy
11243D gChmqcnoesy CNfilt
11322D hbcbcgcdhdA
11423D HC(CO)HN

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-13C; U-15N] cNTnC, 10 mM imidazole, 100 mM potassium chloride, 3 mM N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE, 2.1 mM cTnI(147-163), 15 mM Dithiothreitol (DTT), 0.5 mM DSS, 10 mM calcium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-13C; U-15N] cNTnC, 10 mM imidazole, 100 mM potassium chloride, 9 mM calcium chloride, 2.5 mM N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE, 4.2 mM cTnI(147-163), 15 mM Dithiothreitol (DTT), 0.5 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM [U-13C; U-15N] cNTnC, 10 mM imidazole, 100 mM potassium chloride, 9 mM calcium chloride, 2.8 mM N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE, 2 mM cTnI(147-163), 15 mM Dithiothreitol (DTT), 0.2 mM DSS, 100% D2O100% D2O
40.7 mM [U-13C; U-15N] cNTnC, 10 mM imidazole, 100 mM potassium chloride, 9 mM calcium chloride, 2.9 mM N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE, 3.6 mM cTnI(147-163), 15 mM Dithiothreitol (DTT), 0.4 mM DSS, 100% D2O100% D2O
50.5 mM [U-13C; U-15N] cNTnC, 10 mM imidazole, 100 mM potassium chloride, 9 mM calcium chloride, 3 mM N-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE, 2.2 mM cTnI(147-163), 15 mM Dithiothreitol (DTT), 0.2 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMcNTnC[U-13C; U-15N]1
10 mMimidazole1
100 mMpotassium chloride1
3 mMN-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE1
2.1 mMcTnI(147-163)1
15 mMDithiothreitol (DTT)1
0.5 mMDSS1
10 mMcalcium chloride1
0.8 mMcNTnC[U-13C; U-15N]2
10 mMimidazole2
100 mMpotassium chloride2
9 mMcalcium chloride2
2.5 mMN-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE2
4.2 mMcTnI(147-163)2
15 mMDithiothreitol (DTT)2
0.5 mMDSS2
0.5 mMcNTnC[U-13C; U-15N]3
10 mMimidazole3
100 mMpotassium chloride3
9 mMcalcium chloride3
2.8 mMN-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE3
2 mMcTnI(147-163)3
15 mMDithiothreitol (DTT)3
0.2 mMDSS3
0.7 mMcNTnC[U-13C; U-15N]4
10 mMimidazole4
100 mMpotassium chloride4
9 mMcalcium chloride4
2.9 mMN-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE4
3.6 mMcTnI(147-163)4
15 mMDithiothreitol (DTT)4
0.4 mMDSS4
0.5 mMcNTnC[U-13C; U-15N]5
10 mMimidazole5
100 mMpotassium chloride5
9 mMcalcium chloride5
3 mMN-(6-AMINOHEXYL)-5-CHLORO-1-NAPHTHALENESULFONAMIDE5
2.2 mMcTnI(147-163)5
15 mMDithiothreitol (DTT)5
0.2 mMDSS5
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian UnityVarianUNITY6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, F. et al.processing
NMRViewJohnson, B. et al.chemical shift assignment
NMRViewJohnson, B. et al.data analysis
NMRViewJohnson, B. et al.peak picking
CYANAGuntert, P. et al.chemical shift assignment
TALOSCornilescu, G. et al.dihedral angles calculation
X-PLOR NIHSchwieters, C. et al.structure solution
X-PLOR NIHSchwieters, C. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Protonated form of W7 was used during water refinement. Positive charge on W7 tail (-CH2-NH3+ group) was added manually in analogy to positive charge on -CH2-NH3+ group in LYS+.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20

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