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Yorodumi- PDB-1j1d: Crystal structure of the 46kDa domain of human cardiac troponin i... -
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-Basic information
Entry | Database: PDB / ID: 1j1d | ||||||
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Title | Crystal structure of the 46kDa domain of human cardiac troponin in the Ca2+ saturated form | ||||||
Components |
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Keywords | CONTRACTILE 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 / 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 / muscle filament sliding / transition between fast and slow fiber / negative regulation of ATP-dependent activity / positive regulation of ATP-dependent activity / Striated Muscle Contraction / response to metal ion / regulation of cardiac muscle contraction by calcium ion signaling / regulation of heart contraction / myosin II complex / ventricular cardiac muscle tissue morphogenesis / sarcomere organization / heart contraction / tropomyosin binding / troponin I binding / striated muscle thin filament / skeletal muscle contraction / calcium channel inhibitor activity / vasculogenesis / cardiac muscle contraction / Ion homeostasis / sarcomere / response to calcium ion / 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 / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å | ||||||
Authors | Takeda, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j1d.cif.gz | 156.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j1d.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 1j1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/1j1d ftp://data.pdbj.org/pub/pdb/validation_reports/j1/1j1d | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Chain A, B and C, and chain D, E and F are biological heterotrimer assemblies, respectively. |
-Components
#1: Protein | 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 | 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 | 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 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.72 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2001 Details: KARKPATRIC-BOETZE TYPE RH-COATED DOUBLE MIRROR (SUPER MIRRORS) |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: flat model / Bsol: 51.1 Å2 / ksol: 0.331 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.61→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.61→2.7 Å / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 40 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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