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- EMDB-41124: ISOLATED LETHOCERUS INDICUS Z-DISCS CRYO-EM MAP -

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Basic information

Entry
Database: EMDB / ID: EMD-41124
TitleISOLATED LETHOCERUS INDICUS Z-DISCS CRYO-EM MAP
Map dataThis density map was generated by subtomogram averaging. The C2 connecting density map was generated from this density map.
Sample
  • Complex: Lethocerus Indicus Z-discs
KeywordsZ-discs / Lethocerus / Cryo-EM / Flight muscle / CONTRACTILE PROTEIN
Biological speciesLethocerus indicus (insect)
Methodelectron tomography / cryo EM
AuthorsAbbasi Yeganeh F / Taylor KA
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM030598 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM139616 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10RR025080 United States
National Institutes of Health/Office of the DirectorS10OD018142 United States
American Heart Association15PRE25090150 United States
American Heart Association20PRE35120273 United States
CitationJournal: J Muscle Res Cell Motil / Year: 2023
Title: The cryo-EM 3D image reconstruction of isolated Lethocerus indicus Z-discs.
Authors: Fatemeh Abbasi Yeganeh / Corinne Summerill / Zhongjun Hu / Hamidreza Rahmani / Dianne W Taylor / Kenneth A Taylor /
Abstract: The Z-disk of striated muscle defines the ends of the sarcomere, which repeats many times within the muscle fiber. Here we report application of cryoelectron tomography and subtomogram averaging to Z- ...The Z-disk of striated muscle defines the ends of the sarcomere, which repeats many times within the muscle fiber. Here we report application of cryoelectron tomography and subtomogram averaging to Z-disks isolated from the flight muscles of the large waterbug Lethocerus indicus. We use high salt solutions to remove the myosin containing filaments and use gelsolin to remove the actin filaments of the A- and I-bands leaving only the thin filaments within the Z-disk which were then frozen for cryoelectron microscopy. The Lethocerus Z-disk structure is similar in many ways to the previously studied Z-disk of the honeybee Apis mellifera. At the corners of the unit cell are positioned trimers of paired antiparallel F-actins defining a large solvent channel, whereas at the trigonal positions are positioned F-actin trimers converging slowly towards their (+) ends defining a small solvent channel through the Z-disk. These near parallel F-actins terminate at different Z-heights within the Z-disk. The two types of solvent channel in Lethocerus are similar in size compared to those of Apis which are very different in size. Two types of α-actinin crosslinks were observed between oppositely oriented actin filaments. In one of these, the α-actinin long axis is almost parallel to the F-actins it crosslinks. In the other, the α-actinins are at a small but distinctive angle with respect to the crosslinked actin filaments. The utility of isolated Z-disks for structure determination is discussed.
History
DepositionJun 26, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41124.png

Downloads & links

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Map

FileDownload / File: emd_41124.map.gz / Format: CCP4 / Size: 4.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis density map was generated by subtomogram averaging. The C2 connecting density map was generated from this density map.
Voxel sizeX=Y=Z: 2.14 Å
Density
Minimum - Maximum-0.17536147 - 0.3099094
Average (Standard dev.)-0.000000000029733 (±0.050991215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-100
Dimensions8080200
Spacing8080200
CellA: 171.20001 Å / B: 171.20001 Å / C: 428.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: c5-c3 conecting density map from the subtomogram averaging,...

Fileemd_41124_additional_1.map
Annotationc5-c3 conecting density map from the subtomogram averaging, class averages of the tomograms.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Result of actin filament density map isolated from...

Fileemd_41124_additional_2.map
AnnotationResult of actin filament density map isolated from the tomogram after subtomogram averaging.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The map of the hexagonal lattice of Z-disk...

Fileemd_41124_additional_3.map
AnnotationThe map of the hexagonal lattice of Z-disk after subtomogram averaging
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lethocerus Indicus Z-discs

EntireName: Lethocerus Indicus Z-discs
Components
  • Complex: Lethocerus Indicus Z-discs

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Supramolecule #1: Lethocerus Indicus Z-discs

SupramoleculeName: Lethocerus Indicus Z-discs / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Lethocerus indicus (insect)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 95.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 18000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionDetails: Symmetry not imposed. Symmetry expansion was performed in generating class averages of F-actin.
Number images used: 497

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