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Open data
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Basic information
Entry | Database: PDB / ID: 6klt | ||||||
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Title | Troponin of cardiac thin filament in low-calcium state | ||||||
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![]() | CONTRACTILE PROTEIN / Cardiac thin filament | ||||||
Function / homology | ![]() atrial cardiac muscle tissue morphogenesis / Striated Muscle Contraction / regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / contractile muscle fiber / regulation of ATP-dependent activity / cardiac Troponin complex ...atrial cardiac muscle tissue morphogenesis / Striated Muscle Contraction / regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / regulation of muscle filament sliding speed / troponin T binding / diaphragm contraction / contractile muscle fiber / regulation of ATP-dependent activity / cardiac Troponin complex / cardiac myofibril / actin crosslink formation / troponin complex / regulation of smooth muscle contraction / regulation of muscle contraction / muscle filament sliding / transition between fast and slow fiber / Ion homeostasis / negative regulation of ATP-dependent activity / positive regulation of ATP-dependent activity / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / ventricular cardiac muscle tissue morphogenesis / regulation of heart contraction / sarcomere organization / myofibril / tropomyosin binding / troponin I binding / striated muscle thin filament / skeletal muscle contraction / sarcoplasm / vasculogenesis / calcium channel inhibitor activity / striated muscle contraction / muscle contraction / cardiac muscle contraction / sarcomere / response to bacterium / structural constituent of cytoskeleton / intracellular calcium ion homeostasis / response to calcium ion / calcium-dependent protein binding / actin filament binding / heart development / protein-macromolecule adaptor activity / actin binding / protein domain specific binding / calcium ion binding / protein-containing complex binding / protein kinase binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å | ||||||
![]() | Oda, T. / Yanagisawa, H. / Wakabayashi, T. | ||||||
![]() | ![]() Title: Cryo-EM structures of cardiac thin filaments reveal the 3D architecture of troponin. Authors: Toshiyuki Oda / Haruaki Yanagisawa / Takeyuki Wakabayashi / ![]() Abstract: Troponin is an essential component of striated muscle and it regulates the sliding of actomyosin system in a calcium-dependent manner. Despite its importance, the structure of troponin has been ...Troponin is an essential component of striated muscle and it regulates the sliding of actomyosin system in a calcium-dependent manner. Despite its importance, the structure of troponin has been elusive due to its high structural heterogeneity. In this study, we analyzed the 3D structures of murine cardiac thin filaments using a cryo-electron microscope equipped with a Volta phase plate (VPP). Contrast enhancement by a VPP enabled us to reconstruct the entire repeat of the thin filament. We determined the orientation of troponin relative to F-actin and tropomyosin, and characterized the interactions between troponin and tropomyosin. This study provides a structural basis for understanding the molecular mechanism of actomyosin system. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.7 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 0717MC ![]() 0711C ![]() 0712C ![]() 0714C ![]() 0715C ![]() 0718C ![]() 0796C ![]() 0797C ![]() 0798C ![]() 0799C ![]() 0802C ![]() 0804C ![]() 0805C ![]() 0806C ![]() 0807C ![]() 0808C ![]() 6kllC ![]() 6klnC ![]() 6klpC ![]() 6klqC ![]() 6kluC C: citing same article ( M: map data used to model this data |
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Similar structure data | |
EM raw data | ![]() Data #1: Unaligned multiframe micrographs of cardiac myofilaments in low calcium state [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 16644.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Protein | Mass: 8735.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#3: Protein | Mass: 13524.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
#4: Chemical | Has ligand of interest | Y | Sequence details | Residue GLU 32 could not be modeled due to low resolution. | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: F-actin of cardiac thin filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#3 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1100 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5.6 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 12 Å / Resolution method: OTHER / Num. of particles: 515775 Details: Resolution was estimated based on the comparison between the map and the model-derived map. Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4Y99 Accession code: 4Y99 / Source name: PDB / Type: experimental model |