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- PDB-1lxf: Structure of the Regulatory N-domain of Human Cardiac Troponin C ... -

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Basic information

Entry
Database: PDB / ID: 1lxf
TitleStructure of the Regulatory N-domain of Human Cardiac Troponin C in Complex with Human Cardiac Troponin-I(147-163) and Bepridil
Components
  • TROPONIN C, SLOW SKELETAL AND CARDIAC MUSCLES
  • Troponin I, cardiac muscle
KeywordsMETAL BINDING PROTEIN / PROTEIN BINDING / muscle / cardiac troponin C-drug interaction / bepridil / cardiac troponin I-drug interaction
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 / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / myosin II complex / ventricular cardiac muscle tissue morphogenesis / 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 / Recoverin; domain 1 / 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 / 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-BEP / Troponin I, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, X. / Li, M.X. / Sykes, B.D.
CitationJournal: 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
DepositionJun 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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
Revision 1.4May 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)12,2834
Polymers11,8762
Non-polymers4072
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 #1lowest energy

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Components

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


Mass: 10070.304 Da / Num. of mol.: 1 / Fragment: Regulatory N Domain (residues 1-89)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3plysS) / References: UniProt: P63316
#2: Protein/peptide Troponin I, cardiac muscle /


Mass: 1806.183 Da / Num. of mol.: 1 / Fragment: Switch Peptide (residues 147-163) / Source method: obtained synthetically
Details: The sequence of the protein is naturally found in Homo sapiens. The protein was chemically synthesized.
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-BEP / 1-ISOBUTOXY-2-PYRROLIDINO-3[N-BENZYLANILINO] PROPANE / BEPRIDIL / Bepridil


Mass: 366.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34N2O / Comment: channel blocker*YM

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 15N-separated DIPSI
131(H)CCH-TOCSY
1413D 13C,15N-separated-NOESY
151CBCACONNH
161HN(CA)CB
1712D 13C, 15N-filtered NOESY
1812D 13C, 15N-filtered DIPSI
1913D 13C, 15N-filtered, edited NOESY

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Sample preparation

DetailsContents: 1mM cNTnC, 3mM cTnI147-163, 1.5mM bepridil, 5mM DTT, 100mM KCl, 10mM IMDZ, trace amount of NaN3, 50uM DSS, 90% H2O, 10% D2O
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 software
NameVersionDeveloperClassification
NMRPipe2.1Delaglio, Frankprocessing
NMRView5.0.4Johnson, Brucedata analysis
X-PLOR3.85Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: A total of 1169 NOE restraints, 88 dihedral angle restraints used for the refinement of cNTnC, 30 NOE restraints used between cNTnC and cTnI147-163, 28 NOE restraints used between cNTnC and ...Details: A total of 1169 NOE restraints, 88 dihedral angle restraints used for the refinement of cNTnC, 30 NOE restraints used between cNTnC and cTnI147-163, 28 NOE restraints used between cNTnC and bepridil, 24 intramolecular NOE restraints and 12 dihedral angle restraints used within cTnI147-163.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 30 / Conformers submitted total number: 30

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