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- PDB-1ih0: Structure of the C-domain of Human Cardiac Troponin C in Complex ... -

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Basic information

Entry
Database: PDB / ID: 1ih0
TitleStructure of the C-domain of Human Cardiac Troponin C in Complex with Ca2+ Sensitizer EMD 57033
ComponentsTROPONIN C, SLOW SKELETAL AND CARDIAC MUSCLES
KeywordsCONTRACTILE PROTEIN / Ca2+ binding protein / Ca2+ Sensitizer
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 / response to metal ion ...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 / response to metal ion / ventricular cardiac muscle tissue morphogenesis / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / actin filament binding / calcium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
EF hand / EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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 / EF-hand domain pair / EF-hand / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EMD / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, X. / Li, M.X. / Spyracopoulos, L. / Beier, N. / Chandra, M. / Solaro, R.J. / Sykes, B.D.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Structure of the C-domain of human cardiac troponin C in complex with the Ca2+ sensitizing drug EMD 57033.
Authors: Wang, X. / Li, M.X. / Spyracopoulos, L. / Beier, N. / Chandra, M. / Solaro, R.J. / Sykes, B.D.
History
DepositionApr 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7584
Polymers8,2521
Non-polymers5063
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30all calculated structures submitted
RepresentativeModel #11closest to the minimized average structure

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Components

#1: Protein TROPONIN C, SLOW SKELETAL AND CARDIAC MUSCLES / / TN-C


Mass: 8252.034 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RESIDUES 91-161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: cTnC / Plasmid: pET3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: P63316
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EMD / 5-[1-(3,4-DIMETHOXY-BENZOYL)-1,2,3,4-TETRAHYDRO-QUINOLIN-6-YL]-6-METHYL-3,6-DIHYDRO-[1,3,4]THIADIAZIN-2-ONE


Mass: 425.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23N3O4S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
121HNHB
1313D-13C/15N-NOESY
141HCCHTOCSY
1513D 15N-separated NOESY
161HN(CA)CB
NMR detailsText: The structure of the protein was determined using multidimensional NMR spectroscopy. The structure of EMD 57033 in the complex was determined using 15N/13C-filtered-NOESY and DIPSI experiments. ...Text: The structure of the protein was determined using multidimensional NMR spectroscopy. The structure of EMD 57033 in the complex was determined using 15N/13C-filtered-NOESY and DIPSI experiments. The contacts between protein and EMD 57033 were determined using 15N/13C-filtered/edited experiments.

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Sample preparation

DetailsContents: ~1mM C-domain of Cardiac Troponin C. 100mM KCl 10mM Imidazole 1mM DSS ~1mM EMD 57033 trace DMSO-d6
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.1 / pH: 6.7 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian Unity InovaVarianUnity Inova5001
Varian UNITYVarianUNITY6002
Varian UNITYPLUSVarianUNITYPLUS8003

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Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: Brunger, A. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: ~1000 NOE restraints were used. 61 dihedral restraints as well as 14 NOE restraints between drug and protein.
NMR representativeSelection criteria: closest to the minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 30 / Conformers submitted total number: 30

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