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- PDB-2mle: NMR structure of the C-domain of troponin C bound to the anchorin... -

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Basic information

Entry
Database: PDB / ID: 2mle
TitleNMR structure of the C-domain of troponin C bound to the anchoring region of troponin I
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsMETAL BINDING PROTEIN / troponin C / troponin I / EF-hand / cardiac troponin
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
Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsRobertson, I.M. / Baryshnikova, O.K. / Mercier, P. / Sykes, B.D.
CitationJournal: Biochemistry / Year: 2008
Title: The dilated cardiomyopathy G159D mutation in cardiac troponin C weakens the anchoring interaction with troponin I.
Authors: Baryshnikova, O.K. / Robertson, I.M. / Mercier, P. / Sykes, B.D.
History
DepositionFeb 26, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / 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_database_status.status_code_nmr_data / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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
C: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,4493
Polymers8,3691
Non-polymers802
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 8369.205 Da / Num. of mol.: 1 / Fragment: UNP residues 91-161
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: 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
1112D 1H-15N HSQC
1222D DQF-COSY
1322D 1H-1H NOESY
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HN(CA)CB
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D HNHA
11013D HNHB
11113D 1H-15N NOESY
11213D 1H-15N TOCSY
11313D 1H-13C NOESY
11412D 13C,15N Filtered NOESY
11512D 13C,15N Filtered TOCSY
11613D 13C Edited, Filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-95% 13C; U-95% 15N] cCTnC, 2 mM Calcium, 0.2 mM DSS, 100 mM potassium chloride, 5 mM sodium azide, 10 mM imidazole, 1.2 mM troponin I(34-71), 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-95% 13C; U-95% 15N] cCTnC, 2 mM Calcium, 0.2 mM DSS, 100 mM potassium chloride, 5 mM sodium azide, 0.5 mM imidazole, 1.2 mM troponin I(34-71), 9.5 mM [U-2H] imidazole, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMcCTnC-1[U-95% 13C; U-95% 15N]1
2 mMCalcium-21
0.2 mMDSS-31
100 mMpotassium chloride-41
5 mMsodium azide-51
10 mMimidazole-61
1.2 mMtroponin I(34-71)-71
0.5 mMcCTnC-8[U-95% 13C; U-95% 15N]2
2 mMCalcium-92
0.2 mMDSS-102
100 mMpotassium chloride-112
5 mMsodium azide-122
0.5 mMimidazole-132
1.2 mMtroponin I(34-71)-142
9.5 mMimidazole-15[U-2H]2
Sample conditionsIonic strength: 0.12 / pH: 6.7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian UnityVarianUNITY6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichgeometry optimization
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
ProcheckNMRLaskowski and MacArthurrefinement
ProcheckNMRLaskowski and MacArthurdata analysis
TALOSCornilescu, Delaglio and Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
VnmrJVarianprocessing
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 20

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