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- PDB-7kaa: NMR solution structures of tirasemtiv drug bound to a fast skelet... -

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Basic information

Entry
Database: PDB / ID: 7kaa
TitleNMR solution structures of tirasemtiv drug bound to a fast skeletal troponin C-troponin I complex
ComponentsTroponin C, skeletal muscle,Troponin I, fast skeletal muscle chimera
KeywordsCONTRACTILE PROTEIN / Activator
Function / homology
Function and homology information


relaxation of skeletal muscle / troponin T binding / troponin complex / regulation of muscle contraction / muscle filament sliding / Striated Muscle Contraction / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / actin filament binding ...relaxation of skeletal muscle / troponin T binding / troponin complex / regulation of muscle contraction / muscle filament sliding / Striated Muscle Contraction / skeletal muscle contraction / cardiac muscle contraction / calcium-dependent protein binding / actin filament binding / actin binding / calcium ion binding / positive regulation of DNA-templated transcription / 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
Chem-W97 / Troponin C, skeletal muscle / Troponin I, fast skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMercier, P. / Li, M.X. / Hartman, J.J. / Sykes, B.D.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)37769 Canada
American Heart AssociationG-14-0005884 Canada
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structural Basis of Tirasemtiv Activation of Fast Skeletal Muscle.
Authors: Li, M.X. / Mercier, P. / Hartman, J.J. / Sykes, B.D.
History
DepositionSep 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Troponin C, skeletal muscle,Troponin I, fast skeletal muscle chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3673
Polymers17,0971
Non-polymers2702
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Troponin C, skeletal muscle,Troponin I, fast skeletal muscle chimera / / Troponin I / fast-twitch isoform


Mass: 17096.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC2, TNNI2 / Production host: Escherichia coli (E. coli) / References: UniProt: P02585, UniProt: P48788
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-W97 / 6-ethynyl-1-(pentan-3-yl)-1H-imidazo[4,5-b]pyrazin-2-ol


Mass: 230.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H14N4O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC NH2 only
121isotropic12D 1H-13C HSQC aromatic
131isotropic23D CBCA(CO)NH
141isotropic23D HN(CA)CB
151isotropic23D C(CO)NH
161isotropic23D H(CCO)NH
171isotropic13D 1H-13C NOESY aliphatic
181isotropic13D 1H-15N NOESY aliphatic
191isotropic23D 1H-13C NOESY CNfiltered
1101isotropic22D 1H-15N HSQC CNfiltered

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] TroponinC-Troponin I chimera, 10 mM Imidazole, 100 mM KCl, 90% H2O/10% D2O
Details: 100 mM KCl, 10 mM Imidazole, plus 50 uL 4.96 mM d6-DSS in D2O, 5 uL 1M CaCl2, and 10 uL 1M DTT, pH 6.7
Label: TnC-TnI-tirasemtiv / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMTroponinC-Troponin I chimera[U-13C; U-15N]1
10 mMImidazolenatural abundance1
100 mMKClnatural abundance1
Sample conditionsDetails: dissolved in NMR buffer (100 mM KCl, 10 mM Imidazole), plus 50 uL 4.96 mM d6-DSS in D2O, 5 uL 1M CaCl2, and 10 uL 1M DTT, pH 6.7
Ionic strength: 200 mM / Label: cond1 / pH: 6.7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ3.2Variancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJJohnson, One Moon Scientificchemical shift assignment
NMRViewJJohnson, One Moon Scientificdata analysis
NMRViewJJohnson, One Moon Scientificpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7 / Details: water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 25

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