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- EMDB-17742: In situ actin filament at focal adhesion -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-17742
TitleIn situ actin filament at focal adhesion
Map data
Sample
  • Cell: Mouse embryonic fibroblast
Keywordsfocal adhesion / stress fiber / CELL ADHESION
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 12.0 Å
AuthorsChung WL / Ohad M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: A mixed actin polarity network at focal adhesion
Authors: Chung WL / Ohad M
History
DepositionJun 26, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17742.png

Downloads & links

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Map

FileDownload / File: emd_17742.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 160 pix.
= 353.042 Å		2.21 Å/pix.
x 160 pix.
= 353.042 Å		2.21 Å/pix.
x 160 pix.
= 353.042 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.20651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00907
Minimum - Maximum-0.032014538 - 0.041999955
Average (Standard dev.)0.000020711233 (±0.002850961)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 353.04163 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17742_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17742_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mouse embryonic fibroblast

EntireName: Mouse embryonic fibroblast
Components
  • Cell: Mouse embryonic fibroblast

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Supramolecule #1: Mouse embryonic fibroblast

SupramoleculeName: Mouse embryonic fibroblast / type: cell / ID: 1 / Parent: 0
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 28.0387 Å
Applied symmetry - Helical parameters - Δ&Phi: -167.221 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 891484
ExtractionNumber tomograms: 189 / Number images used: 891484
Final angle assignmentType: ANGULAR RECONSTITUTION

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