+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13999 | ||||||||||||||||||
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Title | Tomogram of skeletal sarcomere I-band after FIB-milling | ||||||||||||||||||
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Sample |
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Keywords | Skeletal muscle / Sarcomere / I-band / CONTRACTILE PROTEIN | ||||||||||||||||||
Biological species | Mus musculus (house mouse) | ||||||||||||||||||
Method | electron tomography / cryo EM | ||||||||||||||||||
Authors | Wang Z / Raunser S | ||||||||||||||||||
Funding support | European Union, 5 items
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Citation | Journal: Science / Year: 2022 Title: Structures from intact myofibrils reveal mechanism of thin filament regulation through nebulin. Authors: Zhexin Wang / Michael Grange / Sabrina Pospich / Thorsten Wagner / Ay Lin Kho / Mathias Gautel / Stefan Raunser / Abstract: In skeletal muscle, nebulin stabilizes and regulates the length of thin filaments, but the underlying mechanism remains nebulous. In this work, we used cryo-electron tomography and subtomogram ...In skeletal muscle, nebulin stabilizes and regulates the length of thin filaments, but the underlying mechanism remains nebulous. In this work, we used cryo-electron tomography and subtomogram averaging to reveal structures of native nebulin bound to thin filaments within intact sarcomeres. This in situ reconstruction provided high-resolution details of the interaction between nebulin and actin, demonstrating the stabilizing role of nebulin. Myosin bound to the thin filaments exhibited different conformations of the neck domain, highlighting its inherent structural variability in muscle. Unexpectedly, nebulin did not interact with myosin or tropomyosin, but it did interact with a troponin T linker through two potential binding motifs on nebulin, explaining its regulatory role. Our structures support the role of nebulin as a thin filament "molecular ruler" and provide a molecular basis for studying nemaline myopathies. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13999.map.gz | 1.2 GB | EMDB map data format | |
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Header (meta data) | emd-13999-v30.xml emd-13999.xml | 13.2 KB 13.2 KB | Display Display | EMDB header |
Images | emd_13999.png | 149.4 KB | ||
Filedesc metadata | emd-13999.cif.gz | 4.1 KB | ||
Others | emd_13999_additional_1.map.gz | 1.2 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13999 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13999 | HTTPS FTP |
-Validation report
Summary document | emd_13999_validation.pdf.gz | 486.2 KB | Display | EMDB validaton report |
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Full document | emd_13999_full_validation.pdf.gz | 485.8 KB | Display | |
Data in XML | emd_13999_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | emd_13999_validation.cif.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13999 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13999 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13999.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.716 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_13999_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Mouse psoas muscle myofibrils
Entire | Name: Mouse psoas muscle myofibrils |
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Components |
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-Supramolecule #1: Mouse psoas muscle myofibrils
Supramolecule | Name: Mouse psoas muscle myofibrils / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 60 / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 2000 / Focused ion beam - Final thickness: 100 Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} 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 K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 3.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.5 µm / Calibrated defocus min: 2.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.5 µm / Nominal defocus min: 2.5 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 |
-Image processing
Final reconstruction | Algorithm: BACK PROJECTION / Number images used: 37 |
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-Atomic model buiding 1
Refinement | Overall B value: 250 |
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