+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0717 | |||||||||
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Title | Troponin of cardiac thin filament in low-calcium state | |||||||||
Map data | Cardiac troponin in low-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 / diaphragm contraction / contractile muscle fiber / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / actin crosslink formation ...atrial cardiac muscle tissue morphogenesis / Striated Muscle Contraction / regulation of systemic arterial blood pressure by ischemic conditions / troponin C binding / diaphragm contraction / contractile muscle fiber / regulation of ATP-dependent activity / regulation of muscle filament sliding speed / troponin T binding / actin crosslink formation / 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 / Ion homeostasis / positive regulation of ATP-dependent activity / regulation of cardiac muscle contraction by calcium ion signaling / response to metal ion / regulation of heart contraction / sarcomere organization / ventricular cardiac muscle tissue morphogenesis / tropomyosin binding / myofibril / heart contraction / troponin I binding / striated muscle thin filament / skeletal muscle contraction / sarcoplasm / striated muscle contraction / calcium channel inhibitor activity / vasculogenesis / cardiac muscle contraction / sarcomere / muscle contraction / response to bacterium / structural constituent of cytoskeleton / intracellular calcium ion homeostasis / response to calcium ion / calcium-dependent protein binding / actin filament binding / protein-macromolecule adaptor activity / actin binding / heart development / protein domain specific binding / calcium ion binding / protein-containing complex binding / protein kinase binding / protein homodimerization activity / identical protein binding / 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_0717.map.gz | 43.2 MB | EMDB map data format | |
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Header (meta data) | emd-0717-v30.xml emd-0717.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0717_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_0717.png | 71.8 KB | ||
Filedesc metadata | emd-0717.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0717 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0717 | HTTPS FTP |
-Related structure data
Related structure data | 6kltMC 0711C 0712C 0714C 0715C 0718C 0796C 0797C 0798C 0799C 0802C 0804C 0805C 0806C 0807C 0808C 6kllC 6klnC 6klpC 6klqC 6kluC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10348 (Title: Cardiac thin filament in low calcium state / Data size: 2.5 TB Data #1: Unaligned multiframe micrographs of cardiac myofilaments in low calcium state [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0717.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 low-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 : F-actin of cardiac thin filament
Entire | Name: F-actin of cardiac thin filament |
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Components |
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-Supramolecule #1: F-actin of cardiac thin filament
Supramolecule | Name: F-actin 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: 16.644533 KDa |
Sequence | String: TEEQKNEFKA AFDIFVLGAD GCISTKELGK VMRMLGQNPT PEELQEMIDE VDEDGSGTVD FDEFLVMMVR CMKDDSKGKS EEELSDLFR MFDKNADGYI DLDELKMMLQ ATGETITEDD IEELMKDGDK NNDGRIDYDE FLEFMK 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: 8.735045 KDa |
Sequence | String: GKRQTEREKK KKILAERRKA LAIDHLNEDQ LREKAKELWQ SIHNLEAEKF DLQEKFKQQK YEINVLRNRI N 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: 13.524673 KDa |
Sequence | String: QLKTLMLQIA KQEMEREAEE RRGEKGRVLR TRCQPLELDG LGFEELQDLC RQLHARVDKV DEERYDVEAK VTKNITEIAD LTQKIYDLR GKFKRPTLRR VRISADAMMQ ALLGTR UniProtKB: Troponin I, cardiac muscle |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 2 / 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.1 µm / Nominal magnification: 81000 |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 5.6 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |