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- PDB-2n7l: NMR structure of the N-domain of troponin C bound to the switch r... -

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Basic information

Entry
Database: PDB / ID: 2n7l
TitleNMR structure of the N-domain of troponin C bound to the switch region of troponin I and the covalent levosimendan analog i9
ComponentsTroponin C/Troponin I chimera
KeywordsCONTRACTILE PROTEIN / troponin C / calcium sensitizer / contraction regulation / levosimendan
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 / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / ventricular cardiac muscle tissue morphogenesis / myosin II complex / 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 domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Troponin I residues 1-32 / Troponin I residues 1-32 / 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, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsPineda Sanabria, S.E. / Sykes, B.D. / Robertson, I.M.
CitationJournal: To be Published
Title: Troponin C with covalently bound levosimendan analog i9 enhances contraction in cardiac muscle fibers
Authors: Pineda Sanabria, S.E. / Robertson, I.M. / Sun, Y. / Irving, M. / Sykes, B.D.
History
DepositionSep 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 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.pdbx_leaving_atom_flag / _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_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/Troponin I chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2582
Polymers16,2181
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Troponin C/Troponin I chimera / TN-C / Cardiac troponin I


Mass: 16218.341 Da / Num. of mol.: 1 / Mutation: C35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC, TNNC1, TNNI3 / Production host: Escherichia coli (E. coli) / References: UniProt: P63316, UniProt: P19429
#2: 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
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D CBCA(CO)NH
1513D HNHA
1623D H(CCO)NH
1723D C(CO)NH
1813D 1H-15N NOESY
1933D 1H-13C NOESY aliphatic
1102gnoesyChsqc CNfilt
11132D 1H-1H NOESY CN filtered
11232D 1H-1H TOCSY
11332D 1H-19F HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.8 mM [U-15N] protein_1, 100 mM potassium chloride, 10 mM imidazole, 2 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 95% H2O/5% D2O95% H2O/5% D2O
20.5-0.8 mM [U-13C; U-15N] protein_1, 100 mM potassium chloride, 10 mM imidazole, 2 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.5-0.8 mM [U-13C; U-15N] protein_1, 100 mM potassium chloride, 10 mM [U-99% 2H] imidazole, 2 mM calcium chloride, 0.25 mM [U-99% 2H] DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-15N]0.5-0.81
100 mMpotassium chloride-21
10 mMimidazole-31
2 mMcalcium chloride-41
0.25 mMDSS-5[U-99% 2H]1
mMentity_1-6[U-13C; U-15N]0.5-0.82
100 mMpotassium chloride-72
10 mMimidazole-82
2 mMcalcium chloride-92
0.25 mMDSS-10[U-99% 2H]2
mMentity_1-11[U-13C; U-15N]0.5-0.83
100 mMpotassium chloride-123
10 mMimidazole-13[U-99% 2H]3
2 mMcalcium chloride-143
0.25 mMDSS-15[U-99% 2H]3
Sample conditionspH: 6.9 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
TALOSCornilescu, Delaglio and Baxprediction of phi and psi dihedral angles
X-PLOR NIH2.35Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.35Schwieters, Kuszewski, Tjandra and Clorerefinement
PRODRGA. W. Sch ttelkopf and D. M. F. van Aaltengeneration of topology and parameter files for non-standard aminoacid ci9
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1284 / NOE intraresidue total count: 794 / NOE medium range total count: 215 / NOE sequential total count: 275 / Protein phi angle constraints total count: 49 / Protein psi angle constraints total count: 50
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.4 Å / Maximum upper distance constraint violation: 0.4 Å

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