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- PDB-1wrk: Crystal structure of the N-terminal domain of human cardiac tropo... -

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Basic information

Entry
Database: PDB / ID: 1wrk
TitleCrystal structure of the N-terminal domain of human cardiac troponin C in complex with trifluoperazine (orthrombic crystal form)
ComponentsTroponin C, slow skeletal and cardiac muscles
KeywordsCONTRACTILE PROTEIN / EF-hand
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 / muscle filament sliding ...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 / muscle filament sliding / response to metal ion / ventricular cardiac muscle tissue morphogenesis / troponin I binding / skeletal muscle contraction / cardiac muscle contraction / sarcomere / 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
Chem-TFP / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsTakeda, S. / Igarashi, T. / Oishi, Y. / Mori, H.
CitationJournal: To be Published
Title: Crystal structure of the N-terminal domain of human cardiac troponin C in complex with trifluoperazine
Authors: Takeda, S. / Igarashi, T. / Oishi, Y. / Mori, H.
History
DepositionOct 20, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Troponin C, slow skeletal and cardiac muscles
B: Troponin C, slow skeletal and cardiac muscles
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6128
Polymers19,9022
Non-polymers1,7106
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.330, 47.900, 98.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 9951.096 Da / Num. of mol.: 2 / Fragment: N-terminal domain / Mutation: C35S, C84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys-S / References: UniProt: P63316
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-TFP / 10-[3-(4-METHYL-PIPERAZIN-1-YL)-PROPYL]-2-TRIFLUOROMETHYL-10H-PHENOTHIAZINE


Mass: 407.496 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H24F3N3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG3350, magnesium chloride, calcium chloride, MES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 11, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 10924 / Num. obs: 10627 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.7
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.357 / % possible all: 89.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DTL

1dtl


Resolution: 2.15→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 551 -RANDOM
Rwork0.23 ---
all0.231 10924 --
obs0.231 10490 96 %-
Displacement parametersBiso mean: 50 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 114 100 1490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_dihedral_angle_d17
LS refinement shellResolution: 2.15→2.23 Å
RfactorNum. reflection% reflection
Rfree0.279 56 -
Rwork0.257 --
obs-946 88.9 %

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