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- PDB-2l1r: The structure of the calcium-sensitizer, dfbp-o, in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2l1r
TitleThe structure of the calcium-sensitizer, dfbp-o, in complex with the N-domain of troponin C and the switch region of troponin I
Components
  • Troponin C
  • Troponin I
KeywordsMETAL BINDING PROTEIN / troponin C / troponin I / Ca2+-sensitizer / dfbp-o / N-domain
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
[(2',4'-difluorobiphenyl-4-yl)oxy]acetic acid / Troponin I, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
HOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRobertson, I.M. / Sun, Y. / Li, M.X. / Sykes, B.D.
CitationJournal: J.MOL.CELL.CARDIOL. / Year: 2010
Title: A structural and functional perspective into the mechanism of Ca(2+)-sensitizers that target the cardiac troponin complex.
Authors: Robertson, I.M. / Sun, Y.B. / Li, M.X. / Sykes, B.D.
History
DepositionAug 3, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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

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Assembly

Deposited unit
A: Troponin C
B: Troponin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5944
Polymers12,2902
Non-polymers3042
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 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Troponin C / TN-C


Mass: 10070.304 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P63316
#2: Protein/peptide Troponin I / Cardiac troponin I


Mass: 2219.701 Da / Num. of mol.: 1 / Fragment: SWITCH REGION / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P19429
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SXK / [(2',4'-difluorobiphenyl-4-yl)oxy]acetic acid


Mass: 264.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10F2O3

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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 H(CCO)NH
1613D HN(CA)CB
1713D 1H-13C NOESY
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11012D 13C, 15N Filtered NOESY
11112D 13C,15N Filtered TOCSY
11212D 1H-19F HOESY
11313D 13C filtered, edited NOESY

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Sample preparation

DetailsContents: 0.5-1 mM [U-99% 13C; U-99% 15N] cNTnC, 2-4 mM cTnI(144-163), 2-4 mM 2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid, 2-4 mM Calcium, 100 mM KCl, 10 mM DTT, 10 mM Imidazole, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMcNTnC[U-99% 13C; U-99% 15N]0.5-11
mMcTnI(144-163)2-41
mM2',4'-difluoro (1,1'-biphenyl)-4-yloxy acetic acid2-41
mMCalcium2-41
100 mMKCl1
10 mMDTT1
10 mMImidazole1
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

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

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Processing

NMR softwareName: X-PLOR NIH / Version: 2.24 / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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