+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0718 | |||||||||
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Title | Troponin of cardiac thin filament in high-calcium state | |||||||||
Map data | Cardiac troponin in high-calcium state | |||||||||
Sample |
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Keywords | Cardiac thin filament / CONTRACTILE PROTEIN | |||||||||
Function / homology | Function and homology information 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 / response to calcium ion / structural constituent of cytoskeleton / actin filament binding / intracellular calcium ion homeostasis / calcium-dependent protein 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 | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Oda T / Yanagisawa H | |||||||||
Citation | Journal: J Struct Biol / Year: 2020 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0718.map.gz | 44.3 MB | EMDB map data format | |
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Header (meta data) | emd-0718-v30.xml emd-0718.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0718_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_0718.png | 72.2 KB | ||
Filedesc metadata | emd-0718.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0718 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0718 | HTTPS FTP |
-Validation report
Summary document | emd_0718_validation.pdf.gz | 402.2 KB | Display | EMDB validaton report |
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Full document | emd_0718_full_validation.pdf.gz | 401.8 KB | Display | |
Data in XML | emd_0718_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | emd_0718_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0718 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0718 | HTTPS FTP |
-Related structure data
Related structure data | 6kluMC 0711C 0712C 0714C 0715C 0717C 0796C 0797C 0798C 0799C 0802C 0804C 0805C 0806C 0807C 0808C 6kllC 6klnC 6klpC 6klqC 6kltC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0718.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cardiac troponin in high-calcium state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Troponin of cardiac thin filament
Entire | Name: Troponin of cardiac thin filament |
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Components |
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-Supramolecule #1: Troponin of cardiac thin filament
Supramolecule | Name: Troponin of cardiac thin filament / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Mus musculus (house mouse) / Strain: ICR / Organ: heart |
-Macromolecule #1: Troponin C, slow skeletal and cardiac muscles
Macromolecule | Name: Troponin C, slow skeletal and cardiac muscles / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 18.021027 KDa |
Sequence | String: DDIYKAAVEQ LTEEQKNEFK AAFDIFVLGA EDGCISTKEL GKVMRMLGQN PTPEELQEMI DEVDEDGSGT VDFDEFLVMM VRCMKDDSK GKSEEELSDL FRMFDKNADG YIDLDELKMM LQATGETITE DDIEELMKDG DKNNDGRIDY DEFLEFMK UniProtKB: Troponin C, slow skeletal and cardiac muscles |
-Macromolecule #2: Troponin T, cardiac muscle
Macromolecule | Name: Troponin T, cardiac muscle / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 9.092364 KDa |
Sequence | String: GKRQTEREKK KKILAERRKA LAIDHLNEDQ LREKAKELWQ SIHNLEAEKF DLQEKFKQQK YEINVLRNRI NDNQ UniProtKB: Troponin T, cardiac muscle |
-Macromolecule #3: Troponin I, cardiac muscle
Macromolecule | Name: Troponin I, cardiac muscle / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 13.812993 KDa |
Sequence | String: LKTLMLQIAK QEMEREAEER RGEKGRVLRT RCQPLELDGL GFEELQDLCR QLHARVDKVD EERYDVEAKV TKNITEIADL TQKIYDLRG KFKRPTLRRV RISADAMMQA LLGTRAKES UniProtKB: Troponin I, cardiac muscle |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.6 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.1 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |