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- PDB-1j1d: Crystal structure of the 46kDa domain of human cardiac troponin i... -

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Basic information

Entry
Database: PDB / ID: 1j1d
TitleCrystal structure of the 46kDa domain of human cardiac troponin in the Ca2+ saturated form
Components
  • Troponin C
  • Troponin I
  • Troponin T
KeywordsCONTRACTILE PROTEIN / Thin filament / muscle regulation / Ca2+ binding protein / EF-hand / coiled-coil
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 Troponin complex / cardiac myofibril / 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 Troponin complex / cardiac myofibril / 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 / tropomyosin binding / regulation of heart contraction / troponin I binding / striated muscle thin filament / skeletal muscle contraction / vasculogenesis / calcium channel inhibitor activity / cardiac muscle contraction / Ion homeostasis / sarcomere / response to calcium ion / intracellular calcium ion homeostasis / calcium-dependent protein binding / actin filament binding / heart development / actin binding / 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 / 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 / EF-hand domain pair / EF-hand / : / Recoverin; domain 1 / 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 / Orthogonal 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 / MAD / Resolution: 2.61 Å
AuthorsTakeda, S. / Yamashita, A. / Maeda, K. / Maeda, Y.
Citation
Journal: Nature / Year: 2003
Title: Structure of the core domain of human cardiac troponin in the Ca2+-saturated form
Authors: Takeda, S. / Yamashita, A. / Maeda, K. / Maeda, Y.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: Structural and functional domains of the troponin complex revealed by limited digestion
Authors: Takeda, S. / Kobayashi, T. / Taniguchi, H. / Hayashi, H. / Maeda, Y.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of troponin C in complex with troponin I fragment at 2.3-A resolution
Authors: Vassylyev, D.G. / Takeda, S. / Wakatsuki, S. / Maeda, K. / Maeda, Y.
History
DepositionDec 3, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Troponin C
B: Troponin T
C: Troponin I
D: Troponin C
E: Troponin T
F: Troponin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,11212
Polymers92,8726
Non-polymers2406
Water1,838102
1
A: Troponin C
B: Troponin T
C: Troponin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5566
Polymers46,4363
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-88 kcal/mol
Surface area20620 Å2
MethodPISA
2
D: Troponin C
E: Troponin T
F: Troponin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5566
Polymers46,4363
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-69 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.346, 167.860, 69.707
Angle α, β, γ (deg.)90.00, 101.35, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain A, B and C, and chain D, E and F are biological heterotrimer assemblies, respectively.

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Components

#1: Protein Troponin C / TNC


Mass: 18401.377 Da / Num. of mol.: 2 / Mutation: C35S, C84S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: cardiac muscle / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P63316
#2: Protein Troponin T / TnT


Mass: 12842.768 Da / Num. of mol.: 2 / Fragment: CNBR fragment, residues 183-288
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: cardiac muscle / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P45379
#3: Protein Troponin I / TNI


Mass: 15191.700 Da / Num. of mol.: 2 / Fragment: Residues 31-163 / Mutation: T31M, C80A, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: cardiac muscle / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plysS / References: UniProt: P19429
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: 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: 3 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, lithium chloride, Tris-HCl, calcium chloride, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %PEG33501reservoir
215 %glycerol1reservoir
30.1 M1reservoirLiCl
450 mMTris-HCl1reservoir
55 mM1reservoirCaCl2or SrCl2, pH8.
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2001
Details: KARKPATRIC-BOETZE TYPE RH-COATED DOUBLE MIRROR (SUPER MIRRORS)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 28863 / Num. obs: 27912 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 14.9
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.223 / % possible all: 84.6
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 40 Å / Num. measured all: 103050
Reflection shell
*PLUS
% possible obs: 84.6 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.61→40 Å / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1362 5 %random
Rwork0.264 ---
all-27881 --
obs-27881 96.3 %-
Solvent computationSolvent model: flat model / Bsol: 51.1 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 73 Å2
Baniso -1Baniso -2Baniso -3
1--18.584 Å20 Å2-1.522 Å2
2--1.605 Å20 Å2
3---16.979 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.61→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5669 0 6 102 5777
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0085
X-RAY DIFFRACTIONc_angle_deg1.398
X-RAY DIFFRACTIONc_dihedral_angle_d18.75
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.3521.5
X-RAY DIFFRACTIONc_mcangle_it2.3582
X-RAY DIFFRACTIONc_scbond_it1.8942
X-RAY DIFFRACTIONc_scangle_it3.1252.5
LS refinement shellResolution: 2.61→2.7 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.36 100 4.3 %
Rwork0.41 2234 -
obs-2334 81.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.75
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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