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- EMDB-30242: Cardiac Z-disc in EGTA+ATP state, F-actin part (see the additiona... -

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Basic information

Entry
Database: EMDB / ID: EMD-30242
TitleCardiac Z-disc in EGTA+ATP state, F-actin part (see the additional maps for the composite map and other components)
Map dataCentral F-actin in EGTA ATP state
Sample
  • Complex: Central F-actin in EGTA+ATP state
Biological speciesSus scrofa domesticus (domestic pig)
Methodsubtomogram averaging / cryo EM / Resolution: 23.0 Å
AuthorsOda T / Yanagisawa H
CitationJournal: Commun Biol / Year: 2020
Title: Cryo-electron tomography of cardiac myofibrils reveals a 3D lattice spring within the Z-discs.
Authors: Toshiyuki Oda / Haruaki Yanagisawa /
Abstract: The Z-disc forms a boundary between sarcomeres, which constitute structural and functional units of striated muscle tissue. Actin filaments from adjacent sarcomeres are cross-bridged by α-actinin in ...The Z-disc forms a boundary between sarcomeres, which constitute structural and functional units of striated muscle tissue. Actin filaments from adjacent sarcomeres are cross-bridged by α-actinin in the Z-disc, allowing transmission of tension across the myofibril. Despite decades of studies, the 3D structure of Z-disc has remained elusive due to the limited resolution of conventional electron microscopy. Here, we observed porcine cardiac myofibrils using cryo-electron tomography and reconstructed the 3D structures of the actin-actinin cross-bridging complexes within the Z-discs in relaxed and activated states. We found that the α-actinin dimers showed contraction-dependent swinging and sliding motions in response to a global twist in the F-actin lattice. Our observation suggests that the actin-actinin complex constitutes a molecular lattice spring, which maintains the integrity of the Z-disc during the muscle contraction cycle.
History
DepositionApr 22, 2020-
Header (metadata) releaseOct 28, 2020-
Map releaseOct 28, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30242.png

Downloads & links

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Map

FileDownload / File: emd_30242.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCentral F-actin in EGTA ATP state
Voxel sizeX=Y=Z: 5.34 Å
Density
Contour LevelBy AUTHOR: 0.046 / Movie #1: 0.012
Minimum - Maximum-0.028291572 - 0.10742737
Average (Standard dev.)0.000558976 (±0.0035362253)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 1068.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.345.345.34
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1068.0001068.0001068.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0280.1070.001

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Supplemental data

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Additional map: Opposite-polarity F-actin in EGTA ATP state

Fileemd_30242_additional_1.map
AnnotationOpposite-polarity F-actin in EGTA ATP state
Projections & Slices
AxesZYX

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Additional map: Opposite-polarity F-actin in EGTA ATP state

Fileemd_30242_additional_10.map
AnnotationOpposite-polarity F-actin in EGTA ATP state
Projections & Slices
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_11.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_12.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_13.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_14.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_15.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_16.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_17.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_18.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_19.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_2.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_20.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Composite map of actin-actinin cross-bridging complex in EGTA...

Fileemd_30242_additional_21.map
AnnotationComposite map of actin-actinin cross-bridging complex in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_3.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Opposite-polarity F-actin in EGTA ATP state

Fileemd_30242_additional_4.map
AnnotationOpposite-polarity F-actin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_5.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_6.map
AnnotationAlpha-actinin in EGTA ATP state
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Additional map: Opposite-polarity F-actin in EGTA ATP state

Fileemd_30242_additional_7.map
AnnotationOpposite-polarity F-actin in EGTA ATP state
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_8.map
AnnotationAlpha-actinin in EGTA ATP state
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Alpha-actinin in EGTA ATP state

Fileemd_30242_additional_9.map
AnnotationAlpha-actinin in EGTA ATP state
Projections & Slices
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Sample components

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Entire : Central F-actin in EGTA+ATP state

EntireName: Central F-actin in EGTA+ATP state
Components
  • Complex: Central F-actin in EGTA+ATP state

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Supramolecule #1: Central F-actin in EGTA+ATP state

SupramoleculeName: Central F-actin in EGTA+ATP state / type: complex / ID: 1 / Parent: 0
Details: Body of the central F-actin in EGAT+ATP state (see additional maps for the actinin bodies and the composite map)
Source (natural)Organism: Sus scrofa domesticus (domestic pig) / Organ: Heart / Organelle: Z-disc

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.2
GridModel: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 99 %
DetailsCardiac myofibrils

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageCooling holder cryogen: NITROGEN
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: 23.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.9) / Number subtomograms used: 8854
ExtractionNumber tomograms: 43 / Number images used: 12925 / Software - Name: PEET
CTF correctionSoftware - Name: IMOD
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.9)
FSC plot (resolution estimation)

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