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- PDB-2mlf: NMR structure of the dilated cardiomyopathy mutation G159D in tro... -

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Basic information

Entry
Database: PDB / ID: 2mlf
TitleNMR structure of the dilated cardiomyopathy mutation G159D in troponin C bound to the anchoring region of troponin I
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsMETAL BINDING PROTEIN / troponin C / dilated cardiomyopathy / G159D / EF-hand
Function / homology
Function and homology information


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 ...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 / 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 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 / : / 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
AuthorsBaryshnikova, O.K. / Robertson, I.M. / 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.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
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)8,5073
Polymers8,4271
Non-polymers802
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 / 50target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 8427.240 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
1213D (H)CCH-TOCSY
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D H(CCO)NH
1613D C(CO)NH
1713D 1H-13C NOESY
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D HNHA
11113D HNHB
11222D DQF-COSY
11322D 1H-1H NOESY
11412D 13C-15N Filtered 1H-1H TOCSY
11512D 13C-15N Filtered 1H-1H NOESY
11612D 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
TALOSCornilescu, Delaglio and Baxdata analysis
TALOSCornilescu, Delaglio and Baxrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
VnmrJVariandata analysis
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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