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- EMDB-11825: In situ subtomogram average of the sarcomeric actin-tropomyosin f... -

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Basic information

Entry
Database: EMDB / ID: EMD-11825
TitleIn situ subtomogram average of the sarcomeric actin-tropomyosin filament from neonatal Wistar rat cardiomyocytes in an intermediate state
Map dataIn situ subtomogram average of the sarcomeric actin filament in complex with tropomyosin in an intermediate state
Sample
  • Complex: Sarcomeric actin-tropomyosin filament in an intermediate state within the native cellular environment of neonatal Wistar rat cardiomyocytes
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 17.7 Å
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
DepositionOct 9, 2020-
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
  • Surface view with section colored by density value
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.24
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11825.png

Downloads & links

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Map

FileDownload / File: emd_11825.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ subtomogram average of the sarcomeric actin filament in complex with tropomyosin in an intermediate state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 128 pix.
= 437.76 Å		3.42 Å/pix.
x 128 pix.
= 437.76 Å		3.42 Å/pix.
x 128 pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24 / Movie #1: 0.24
Minimum - Maximum-0.37933558 - 0.70001704
Average (Standard dev.)-0.00028961914 (±0.051435664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z437.760437.760437.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.3790.700-0.000

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Supplemental data

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Mask #1

Fileemd_11825_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 1

Fileemd_11825_half_map_1.map
AnnotationHalfmap 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap 2

Fileemd_11825_half_map_2.map
AnnotationHalfmap 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Sarcomeric actin-tropomyosin filament in an intermediate state wi...

EntireName: Sarcomeric actin-tropomyosin filament in an intermediate state within the native cellular environment of neonatal Wistar rat cardiomyocytes
Components
  • Complex: Sarcomeric actin-tropomyosin filament in an intermediate state within the native cellular environment of neonatal Wistar rat cardiomyocytes

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Supramolecule #1: Sarcomeric actin-tropomyosin filament in an intermediate state wi...

SupramoleculeName: Sarcomeric actin-tropomyosin filament in an intermediate state within the native cellular environment of neonatal Wistar rat cardiomyocytes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Heart / Location in cell: Cytoplasm

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 17.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP (ver. 0.7) / Number subtomograms used: 27030
ExtractionNumber tomograms: 10 / Number images used: 160617 / Software: (Name: AmiraFPM, MATLAB)
CTF correctionSoftware: (Name: CTFFIND (ver. 4), NOVACTF)
Final angle assignmentType: NOT APPLICABLE / Software - Name: STOPGAP (ver. 0.7)
FSC plot (resolution estimation)

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