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- PDB-1npq: structure of a rhodamine-labeled N-domain Troponin C mutant (Ca2+... -

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Basic information

Entry
Database: PDB / ID: 1npq
Titlestructure of a rhodamine-labeled N-domain Troponin C mutant (Ca2+ saturated) in complex with skeletal Troponin I 115-131
Components
  • Troponin C
  • Troponin I
KeywordsSTRUCTURAL PROTEIN / Troponin C- Troponin I complex / bifunctional rhodamine labeled Toponin C
Function / homology
Function and homology information


troponin T binding / Striated Muscle Contraction / troponin complex / skeletal muscle contraction / cardiac muscle contraction / actin binding / calcium ion binding
Similarity search - Function
: / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif ...: / 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
Troponin C, skeletal muscle / Troponin I, fast skeletal muscle
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing using torsion angle dynamics, cartesian dynamics with the program CNS 1.1
Model type detailsminimized average
AuthorsMercier, P. / Ferguson, R.E. / Irving, M. / Corrie, J.E.T. / Trentham, D.R. / Sykes, B.D.
CitationJournal: Biochemistry / Year: 2003
Title: NMR Structure of a Bifunctional Rhodamine Labeled N-Domain of Troponin C Complexed with the Regulatory "Switch" Peptide from Troponin I: Implications for in Situ Fluorescence Studies in Muscle Fibers
Authors: Mercier, P. / Ferguson, R.E. / Irving, M. / Corrie, J.E.T. / Trentham, D.R. / Sykes, B.D.
History
DepositionJan 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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_ref_seq_dif / 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_ref_seq_dif.details / _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
A: Troponin C
B: Troponin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9034
Polymers11,8222
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Troponin C / Troponin C / skeletal muscle


Mass: 9932.144 Da / Num. of mol.: 1 / Fragment: TnC, residues 1-90 / Mutation: E56C, E63C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TNNC2 / Plasmid: pET3asNTnC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02588
#2: Protein/peptide Troponin I / Troponin I / fast skeletal muscle / Troponin I / fast-twitch isoform


Mass: 1890.303 Da / Num. of mol.: 1 / Fragment: switch peptide, residues 115-131 / Source method: obtained synthetically
Details: This sequence occurs naturally in Oryctolagus cuniculus (rabit)
References: UniProt: P02643
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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/13C-NOESY
131HNHA
1412D 13C/15N-edited-NOESY
1512D 13C/15N-filtered/edited-NOESY
NMR detailsText: The structure was determined using triple-resonance spectroscopy. The chemical shifts for TnI115-131 were obtained from a 2D_15N/13C_filtered-DIPSI experiment. Intramolecular NOEs for TnI115- ...Text: The structure was determined using triple-resonance spectroscopy. The chemical shifts for TnI115-131 were obtained from a 2D_15N/13C_filtered-DIPSI experiment. Intramolecular NOEs for TnI115-131 were obtained from a 2D_15N/13C_filtered-NOESY experiment.

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Sample preparation

DetailsContents: 320 mM KCl, 10 mM imidazole, 1.3% NaN3, pH 6.5, ~1mM sNTnC.2Ca2+.TnI115-131.BR56-63
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 320 mM KCl / pH: 6.5 / Pressure: ambiant / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
NameVersionDeveloperClassification
CNS1.1A.T.Brungerstructure solution
NMRPipeFeb 2002Frank Delaglioprocessing
NMRView5.0.4Bruce Johnsondata analysis
Procheck3.5.4Laskowskidata analysis
CNS1.1A.T.Brungerrefinement
RefinementMethod: simulated annealing using torsion angle dynamics, cartesian dynamics with the program CNS 1.1
Software ordinal: 1
Details: calcium restraints were introduced only during the 2nd cooling stage using cartesian dynamics. See table 3 of the reference paper for a detailed description of the distance and dihedral restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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