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Yorodumi- EMDB-12572: Tomogram of myofibrils within a native neonatal Wistar rat cardio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12572 | |||||||||
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Title | Tomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte | |||||||||
Map data | Tomogram of a myofibril from neonatal Wistar rat cardiomyocytes | |||||||||
Sample |
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Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Schneider J / Burbaum L / Jasnin M | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Molecular-scale visualization of sarcomere contraction within native cardiomyocytes. Authors: Laura Burbaum / Jonathan Schneider / Sarah Scholze / Ralph T Böttcher / Wolfgang Baumeister / Petra Schwille / Jürgen M Plitzko / Marion Jasnin / Abstract: Sarcomeres, the basic contractile units of striated muscle, produce the forces driving muscular contraction through cross-bridge interactions between actin-containing thin filaments and myosin II- ...Sarcomeres, the basic contractile units of striated muscle, produce the forces driving muscular contraction through cross-bridge interactions between actin-containing thin filaments and myosin II-based thick filaments. Until now, direct visualization of the molecular architecture underlying sarcomere contractility has remained elusive. Here, we use in situ cryo-electron tomography to unveil sarcomere contraction in frozen-hydrated neonatal rat cardiomyocytes. We show that the hexagonal lattice of the thick filaments is already established at the neonatal stage, with an excess of thin filaments outside the trigonal positions. Structural assessment of actin polarity by subtomogram averaging reveals that thin filaments in the fully activated state form overlapping arrays of opposite polarity in the center of the sarcomere. Our approach provides direct evidence for thin filament sliding during muscle contraction and may serve as a basis for structural understanding of thin filament activation and actomyosin interactions inside unperturbed cellular environments. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12572.map.gz | 230.4 MB | EMDB map data format | |
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Header (meta data) | emd-12572-v30.xml emd-12572.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
Images | emd_12572.png | 139.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12572 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12572 | HTTPS FTP |
-Validation report
Summary document | emd_12572_validation.pdf.gz | 202.9 KB | Display | EMDB validaton report |
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Full document | emd_12572_full_validation.pdf.gz | 202 KB | Display | |
Data in XML | emd_12572_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | emd_12572_validation.cif.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12572 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12572 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12572.map.gz / Format: CCP4 / Size: 287.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tomogram of a myofibril from neonatal Wistar rat cardiomyocytes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 13.68 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 : Tomogram of myofibrils within a native neonatal Wistar rat cardio...
Entire | Name: Tomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte |
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Components |
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-Supramolecule #1: Tomogram of myofibrils within a native neonatal Wistar rat cardio...
Supramolecule | Name: Tomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) / Organ: Heart |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.03 nA / Focused ion beam - Duration: 300 sec. / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 400 nm / Focused ion beam - Final thickness: 180 nm Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Quanta 3D FIB/SEM (Thermo Fisher Scientific). This is not in a list of allowed values {'OTHER', 'DB235'} ...Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Quanta 3D FIB/SEM (Thermo Fisher Scientific). This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 120.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Software - Name: IMOD Details: The tomogram was reconstructed in IMOD, binned by a factor of 4, and filtered using a deconvolution filter (https://github.com/dtegunov/tom_deconv) Number images used: 60 |
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