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- EMDB-12572: Tomogram of myofibrils within a native neonatal Wistar rat cardio... -

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Basic information

Entry
Database: EMDB / ID: EMD-12572
TitleTomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte
Map dataTomogram of a myofibril from neonatal Wistar rat cardiomyocytes
Sample
  • Cell: Tomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte
Biological speciesRattus norvegicus (Norway rat)
Methodelectron tomography / cryo EM
AuthorsSchneider J / Burbaum L / Jasnin M
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Federal Ministry for Education and Research81Z1600313 Germany
CitationJournal: 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
DepositionMar 8, 2021-
Header (metadata) releaseMay 12, 2021-
Map releaseMay 12, 2021-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_12572.png

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Map

FileDownload / File: emd_12572.map.gz / Format: CCP4 / Size: 287.5 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationTomogram of a myofibril from neonatal Wistar rat cardiomyocytes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
13.68 Å/pix.
x 175 pix.
= 2394. Å		13.68 Å/pix.
x 928 pix.
= 12695.04 Å		13.68 Å/pix.
x 928 pix.
= 12695.04 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 13.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-12102.0 - 5216.0
Average (Standard dev.)470.24664 (±460.6295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928175
Spacing928928175
CellA: 12695.04 Å / B: 12695.04 Å / C: 2394.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z13.6813.6813.68
M x/y/z928928175
origin x/y/z0.0000.0000.000
length x/y/z12695.04012695.0402394.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS928928175
D min/max/mean-12102.0005216.000470.247

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Supplemental data

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Sample components

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Entire : Tomogram of myofibrils within a native neonatal Wistar rat cardio...

EntireName: Tomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte
Components
  • Cell: Tomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte

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Supramolecule #1: Tomogram of myofibrils within a native neonatal Wistar rat cardio...

SupramoleculeName: Tomogram of myofibrils within a native neonatal Wistar rat cardiomyocyte
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Heart

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: 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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