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- PDB-1sbj: NMR Structure of the Mg2+-loaded C Terminal Domain of Cardiac Tro... -

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Basic information

Entry
Database: PDB / ID: 1sbj
TitleNMR Structure of the Mg2+-loaded C Terminal Domain of Cardiac Troponin C Bound to the N Terminal Domain of Cardiac Troponin I
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsCONTRACTILE PROTEIN / STRUCTURAL PROTEIN / TROPONIN C-TROPONIN I INTERACTION / CARDIAC / MUSCLE PROTEIN / 2 MAGNESIUM BINDING PROTEIN
Function / homology
Function and homology information


cardiac Troponin complex / Striated Muscle Contraction / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / calcium ion binding
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 / 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
Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / DGSA
AuthorsFinley, N.L. / Howarth, J.W. / Rosevear, P.R.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of the Mg2+-loaded C-lobe of cardiac troponin C bound to the N-domain of cardiac troponin I: comparison with the Ca2+-loaded structure.
Authors: Finley, N.L. / Howarth, J.W. / Rosevear, P.R.
History
DepositionFeb 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOR: AUTHOR
Remark 700SHEET DETERMINATION METHOR: AUTHOR

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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)9,5123
Polymers9,4641
Non-polymers492
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 / 20structures with the lowest energy
RepresentativeModel #11lowest energy

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Components

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


Mass: 9463.531 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (RESIDUES 81 - 161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: cTnC / Plasmid: PET-23D+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09860
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
121HNHA, HNHB, CN-NOESY-HSQC
131(HB)CBCA(CO)NH, HN(CA)CB
141H(CCO)NH,C(CO)NH
151(HB)CB(CGCD)HD, (HB)CB(CGCDCE)HE
161NOESY-HSQC, AB-TROSY
NMR detailsText: Best 20 Structures. These structures were determined using triple-resonance NMR spectroscopy on Mg2+-saturated 15N,13C-cTnC(81-161) bound to cTnI(33-80).

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [13C,15]cTnC(81-161)/cTnI(33-80), 20mM Tris(d11), 10mM DTT, 20mM beta-mercaptoethanol, 2mM EGTA, 100mM KCl, 20mM MgCl2, 90% H20, 10% D2O90% H20, 10% D2O
21mM [15N]cTnC(81-161)/cTnI(33-80), 20mM Tris(d11), 10mM DTT, 20mM beta-mercaptoethanol, 2mM EGTA, 100mM KCl, 20mM MgCl2, 90% H20, 10% D2O90% H20, 10% D2O
Sample conditionsIonic strength: 100 mM CaCl2, 20 mM MgCl2 / pH: 6.8 / Pressure: ambient / Temperature: 318.00 K

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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 INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000Accelrysprocessing
CNS1Brungerstructure solution
CNX1Accelrysstructure solution
CNX1Accelrysrefinement
RefinementMethod: DGSA / Software ordinal: 1
Details: the structures are based on a total of 958 restraints, 818 are NOE-derived distance restraints, 78 dihedral angle restraints, 4 distance restraints from hydrogen bonds and 58 dipolar coupling restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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