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- PDB-2mkp: N domain of cardiac troponin C bound to the switch fragment of fa... -

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Basic information

Entry
Database: PDB / ID: 2mkp
TitleN domain of cardiac troponin C bound to the switch fragment of fast skeletal troponin I at pH 6
Components
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, fast skeletal muscle
KeywordsMETAL BINDING PROTEIN / troponin C / troponin I / EF-hand / Calcium binding / Ischemia
Function / homology
Function and homology information


relaxation of skeletal muscle / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / cardiac Troponin complex / troponin complex / regulation of muscle contraction / transition between fast and slow fiber / Striated Muscle Contraction ...relaxation of skeletal muscle / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / regulation of ATP-dependent activity / 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 / myosin II complex / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / actin filament binding / actin binding / calcium ion binding / positive regulation of DNA-templated transcription / protein homodimerization activity / nucleus / cytosol
Similarity search - Function
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
Troponin I, fast skeletal muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsRobertson, I.M. / Pineda-Sanabria, S.E. / Holmes, P.C. / Sykes, B.D.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: Conformation of the critical pH sensitive region of troponin depends upon a single residue in troponin I.
Authors: Robertson, I.M. / Pineda-Sanabria, S.E. / Holmes, P.C. / Sykes, B.D.
History
DepositionFeb 11, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_struct_conn_angle / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,9733
Polymers11,9332
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

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


Mass: 10070.304 Da / Num. of mol.: 1 / Fragment: UNP residues 1-89
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC / Production host: Escherichia coli (E. coli) / References: UniProt: P63316
#2: Protein/peptide Troponin I, fast skeletal muscle / Troponin I / fast-twitch isoform


Mass: 1862.289 Da / Num. of mol.: 1 / Fragment: UNP residues 116-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI2 / Production host: Escherichia coli (E. coli) / References: UniProt: P48788
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / 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
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HN(CA)CB
1613D H(CCO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1912D 1H-1H NOESY
11012D 1H-1H TOCSY

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Sample preparation

DetailsContents: 0.2-0.3 mM [U-95% 13C; U-95% 15N] cNTnC, 2-2.5 mM sTnI(115-131), 0.25 mM DSS, 100 mM potassium chloride, 10 mM imidazole, 10 mM Calcium, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMcNTnC-1[U-95% 13C; U-95% 15N]0.2-0.31
mMsTnI(115-131)-22-2.51
0.25 mMDSS-31
100 mMpotassium chloride-41
10 mMimidazole-51
10 mMCalcium-61
Sample conditionsIonic strength: 0.12 / pH: 6.00 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UnityVarianUNITY6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
PSVSBhattacharya and Montelionerefinement
PSVSBhattacharya and Montelionedata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: semi-rigid simulated annealing. sTnI was docked onto cNTnC. cNTnC backbone was kept rigid and side chain's were allowed to rotate.
NMR constraintsNOE constraints total: 274 / NOE intraresidue total count: 99 / NOE long range total count: 54 / NOE medium range total count: 56 / NOE sequential total count: 65 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 6 / Protein psi angle constraints total count: 7
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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