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- PDB-4y99: Core domain of human cardiac troponin -

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Basic information

Entry
Database: PDB / ID: 4y99
TitleCore domain of human cardiac troponin
Components
  • Troponin C, slow skeletal and cardiac muscles
  • Troponin I, cardiac muscle
  • Troponin T, cardiac muscle
KeywordsCONTRACTILE PROTEIN / muscle regulation / calcium-binding / EF-hand / coiled-coil / myopathy / complex
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of muscle contraction ...regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / cardiac myofibril / cardiac Troponin complex / troponin complex / regulation of muscle contraction / regulation of smooth muscle contraction / negative regulation of ATP-dependent activity / transition between fast and slow fiber / positive regulation of ATP-dependent activity / Striated Muscle Contraction / muscle filament sliding / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / ventricular cardiac muscle tissue morphogenesis / heart contraction / regulation of heart contraction / tropomyosin binding / troponin I binding / striated muscle thin filament / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / Ion homeostasis / cardiac muscle contraction / sarcomere / intracellular calcium ion homeostasis / response to calcium ion / calcium-dependent protein binding / actin filament binding / actin binding / heart development / protein domain specific binding / calcium ion binding / protein kinase binding / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
Troponin complex, TnI/TnT subunit / Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / : ...Troponin complex, TnI/TnT subunit / Troponin T / Troponin I residues 1-32 / Troponin I residues 1-32 / : / Troponin / Troponin domain superfamily / Troponin / EF-hand domain pair / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Troponin I, cardiac muscle / Troponin T, cardiac muscle / Troponin C, slow skeletal and cardiac muscles
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsTakeda, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
The ministry of Education, Culture, Sports, Science and Techinology Japan Japan
CitationJournal: To Be Published
Title: Core domain of human cardiac troponin
Authors: Takeda, S. / Fujiwara, S.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,82812
Polymers55,2393
Non-polymers5899
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11580 Å2
ΔGint-94 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.062, 80.368, 93.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

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


Mass: 18401.377 Da / Num. of mol.: 1 / Mutation: C35S, C84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNC1, TNNC / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P63316
#2: Protein Troponin T, cardiac muscle / TnTc / Cardiac muscle troponin T / cTnT


Mass: 12842.768 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 193-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNT2 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P45379
#3: Protein Troponin I, cardiac muscle / Cardiac troponin I


Mass: 23994.553 Da / Num. of mol.: 1 / Mutation: C80A, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3, TNNC1 / Plasmid: pET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P19429

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Non-polymers , 3 types, 111 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Dimethy sulfoxide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. obs: 31896 / % possible obs: 97.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 5.9 / % possible all: 83.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J1D

1j1d


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.042 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1680 5 %RANDOM
Rwork0.2302 ---
obs0.2317 31896 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 100.06 Å2 / Biso mean: 46.459 Å2 / Biso min: 20.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---2.71 Å20 Å2
3---2.85 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 27 102 3000
Biso mean--73.1 42.83 -
Num. residues----355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222912
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.9913880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2355350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53825.605157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82315605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1131523
X-RAY DIFFRACTIONr_chiral_restr0.0670.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022154
X-RAY DIFFRACTIONr_mcbond_it0.7321.51764
X-RAY DIFFRACTIONr_mcangle_it1.47722818
X-RAY DIFFRACTIONr_scbond_it2.43831148
X-RAY DIFFRACTIONr_scangle_it4.3844.51062
LS refinement shellResolution: 1.996→2.048 Å
RfactorNum. reflection% reflection
Rfree0.339 100 5 %
Rwork0.28 1911 -
obs--80.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79880.5582-0.00071.12580.20220.06580.00910.05780.15010.203-0.02620.20640.06490.00930.01710.09350.00590.03540.083-0.00610.116757.937485.517733.8367
20.16440.5627-0.15032.1071-0.58040.1841-0.01880.0069-0.0117-0.0095-0.0288-0.10870.0014-0.01090.04760.0529-0.00090.01690.04980.01140.141141.960141.928623.9958
30.2530.36540.01151.150.02130.00560.05070.03320.01640.1957-0.02980.11920.0091-0.004-0.02080.1015-0.02690.03110.04770.01350.104448.844659.37932.2894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 161
2X-RAY DIFFRACTION2B199 - 272
3X-RAY DIFFRACTION3C31 - 137

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