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- EMDB-12292: In situ structure of the I-band thin filament excluding troponin ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12292
TitleIn situ structure of the I-band thin filament excluding troponin from mouse psoas muscle
Map data
Sample
  • Complex: I-band thin filament excluding troponin from mouse psoas muscle
    • Complex: actin
    • Complex: tropomyosin
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 10.6 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.
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: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12292.png

Downloads & links

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Map

FileDownload / File: emd_12292.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.51 Å/pix.
x 100 pix.
= 351. Å		3.51 Å/pix.
x 100 pix.
= 351. Å		3.51 Å/pix.
x 100 pix.
= 351. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.51 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.095972985 - 0.2048108
Average (Standard dev.)0.0006342992 (±0.013946016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 351.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.513.513.51
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z351.000351.000351.000
α/β/γ90.00090.00090.000
start NX/NY/NZ278280246
NX/NY/NZ474891
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0960.2050.001

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Supplemental data

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Mask #1

Fileemd_12292_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_12292_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_12292_half_map_2.map
Projections & Slices
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Sample components

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Entire : I-band thin filament excluding troponin from mouse psoas muscle

EntireName: I-band thin filament excluding troponin from mouse psoas muscle
Components
  • Complex: I-band thin filament excluding troponin from mouse psoas muscle
    • Complex: actin
    • Complex: tropomyosin

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Supramolecule #1: I-band thin filament excluding troponin from mouse psoas muscle

SupramoleculeName: I-band thin filament excluding troponin from mouse psoas muscle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: actin

SupramoleculeName: actin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: tropomyosin

SupramoleculeName: tropomyosin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#6
Source (natural)Organism: Mus musculus (house mouse)

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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
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
140.0 mMKClpotassium chloride
2.0 mMMgCl2magnesium chloride
1.0 mMEGTAegtazic acid
1.0 mMDTTdithiothreitol
GridModel: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was myofibrils.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-8 / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 28409 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.4) / Number subtomograms used: 15153
ExtractionNumber tomograms: 4 / Number images used: 15153
CTF correctionSoftware - Name: IMOD
Final 3D classificationSoftware - Name: RELION (ver. 3.0.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6kn8

RefinementProtocol: RIGID BODY FIT

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