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- EMDB-12289: Structure of the in situ actomyosin complex from the A-band of mo... -

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Basic information

Entry
Database: EMDB / ID: EMD-12289
TitleStructure of the in situ actomyosin complex from the A-band of mouse psoas muscle sarcomere in the rigor state obtained by sub-tomogram averaging
Map data
SampleIn situ actomyosin complex in the rigor state from mouse psoas muscle
  • actin
  • myosin double head
  • tropomyosin
  • Actin, alpha skeletal muscle
  • Tropomyosin alpha-1 chain
  • Myosin-4
  • Myosin light chain 1/3, skeletal muscle isoform
  • Myosin regulatory light chain 2, skeletal muscle isoform
Function / homology
Function and homology information


skeletal muscle fiber adaptation / muscle thin filament tropomyosin / positive regulation of heart rate by epinephrine / contractile fiber / regulation of ATPase activity / dynactin complex / cellular response to organonitrogen compound / response to extracellular stimulus / myosin filament / ruffle organization ...skeletal muscle fiber adaptation / muscle thin filament tropomyosin / positive regulation of heart rate by epinephrine / contractile fiber / regulation of ATPase activity / dynactin complex / cellular response to organonitrogen compound / response to extracellular stimulus / myosin filament / ruffle organization / actin filament capping / positive regulation of ATPase activity / muscle filament sliding / structural constituent of muscle / myosin complex / ventricular cardiac muscle tissue morphogenesis / mesenchyme migration / myofibril / skeletal muscle thin filament assembly / striated muscle thin filament / response to lithium ion / motor activity / cardiac muscle contraction / skeletal muscle tissue development / skeletal muscle fiber development / positive regulation of cell adhesion / stress fiber / positive regulation of stress fiber assembly / sarcomere / negative regulation of cell migration / filopodium / response to activity / actin filament / actin filament organization / response to mechanical stimulus / structural constituent of cytoskeleton / muscle contraction / response to steroid hormone / cell body / actin filament binding / actin cytoskeleton / double-stranded RNA binding / lamellipodium / wound healing / disordered domain specific binding / actin binding / protein N-terminus binding / in utero embryonic development / calmodulin binding / immune response / protein heterodimerization activity / positive regulation of gene expression / calcium ion binding / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm
in:ipr027401: / Actin family / IQ motif, EF-hand binding site / Tropomyosin / Myosin head, motor domain / EF-hand domain / Kinesin motor domain superfamily / ATPase, nucleotide binding domain / Myosin tail / Actin, conserved site ...in:ipr027401: / Actin family / IQ motif, EF-hand binding site / Tropomyosin / Myosin head, motor domain / EF-hand domain / Kinesin motor domain superfamily / ATPase, nucleotide binding domain / Myosin tail / Actin, conserved site / EF-hand domain pair / Myosin, N-terminal, SH3-like / Actin/actin-like conserved site / EF-Hand 1, calcium-binding site / P-loop containing nucleoside triphosphate hydrolase / Myosin S1 fragment, N-terminal
Myosin light chain 1/3, skeletal muscle isoform / Tropomyosin alpha-1 chain / Actin, alpha skeletal muscle / Myosin regulatory light chain 2, skeletal muscle isoform / Myosin-4
Biological speciesMus musculus (house mouse) / Mouse (mice)
Methodsubtomogram averaging / cryo EM / Resolution: 10.2 Å
AuthorsWang Z / Grange M / Wagner T / Kho AL / Gautel M / Raunser S
Funding support Germany, United Kingdom, European Union, 5 items
OrganizationGrant numberCountry
Max Planck Society Germany
Wellcome Trust201543/Z/16/Z United Kingdom
European Research Council (ERC)856118European Union
Medical Research Council (MRC, United Kingdom)MR/R003106/1 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 693-2018European Union
CitationJournal: Cell / Year: 2021
Title: The molecular basis for sarcomere organization in vertebrate skeletal muscle.
Authors: Zhexin Wang / Michael Grange / Thorsten Wagner / Ay Lin Kho / Mathias Gautel / Stefan Raunser /
Abstract: Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we ...Sarcomeres are force-generating and load-bearing devices of muscles. A precise molecular picture of how sarcomeres are built underpins understanding their role in health and disease. Here, we determine the molecular architecture of native vertebrate skeletal sarcomeres by electron cryo-tomography. Our reconstruction reveals molecular details of the three-dimensional organization and interaction of actin and myosin in the A-band, I-band, and Z-disc and demonstrates that α-actinin cross-links antiparallel actin filaments by forming doublets with 6-nm spacing. Structures of myosin, tropomyosin, and actin at ~10 Å further reveal two conformations of the "double-head" myosin, where the flexible orientation of the lever arm and light chains enable myosin not only to interact with the same actin filament, but also to split between two actin filaments. Our results provide unexpected insights into the fundamental organization of vertebrate skeletal muscle and serve as a strong foundation for future investigations of muscle diseases.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionFeb 4, 2021-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7nep
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7nep
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12289.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.76 Å/pix.
x 200 pix.
= 351. Å
1.76 Å/pix.
x 200 pix.
= 351. Å
1.76 Å/pix.
x 200 pix.
= 351. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.755 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.02
Minimum - Maximum-0.06538552 - 0.099714175
Average (Standard dev.)0.0005608661 (±0.0068937363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 351.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7551.7551.755
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z351.000351.000351.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0650.1000.001

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Supplemental data

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Segmentation: #1

Fileemd_12289_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 2

Fileemd_12289_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1

Fileemd_12289_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire In situ actomyosin complex in the rigor state from mouse psoas muscle

EntireName: In situ actomyosin complex in the rigor state from mouse psoas muscle
Number of components: 9

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Component #1: protein, In situ actomyosin complex in the rigor state from mouse...

ProteinName: In situ actomyosin complex in the rigor state from mouse psoas muscle
Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)

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Component #2: protein, actin

ProteinName: actin / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)

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Component #3: protein, myosin double head

ProteinName: myosin double head / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)

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Component #4: protein, tropomyosin

ProteinName: tropomyosin / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)

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Component #5: protein, Actin, alpha skeletal muscle

ProteinName: Actin, alpha skeletal muscle / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 41.747527 kDa
SourceSpecies: Mouse (mice)

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Component #6: protein, Tropomyosin alpha-1 chain

ProteinName: Tropomyosin alpha-1 chain / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 28.922074 kDa
SourceSpecies: Mouse (mice)

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Component #7: protein, Myosin-4

ProteinName: Myosin-4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 92.518234 kDa
SourceSpecies: Mouse (mice)

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Component #8: protein, Myosin light chain 1/3, skeletal muscle isoform

ProteinName: Myosin light chain 1/3, skeletal muscle isoform / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.57359 kDa
SourceSpecies: Mouse (mice)

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Component #9: protein, Myosin regulatory light chain 2, skeletal muscle isoform

ProteinName: Myosin regulatory light chain 2, skeletal muscle isoform
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.326439 kDa
SourceSpecies: Mouse (mice)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 286 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 3.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal), 28409 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 18090
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 10.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 5JLH, 6KN8, 3I5G
Output model

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