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- EMDB-11976: Actin filament structure from focal adhesions of mouse embryonic ... -

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Basic information

Entry
Database: EMDB / ID: EMD-11976
TitleActin filament structure from focal adhesions of mouse embryonic fibroblasts
Map dataActin filament structure from focal adhesions of mouse embryonic fibroblasts
Sample
  • Complex: Actin filament from focal adhesions of mouse embryonic fibroblastsMicrofilament
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 17.0 Å
AuthorsMartins B / Medalia O / Eibauer M
Funding support Switzerland, European Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_179418 Switzerland
European Research Council (ERC)810057-HighResCellsEuropean Union
CitationJournal: Structure / Year: 2021
Title: Unveiling the polarity of actin filaments by cryo-electron tomography.
Authors: Bruno Martins / Simona Sorrentino / Wen-Lu Chung / Meltem Tatli / Ohad Medalia / Matthias Eibauer /
Abstract: The actin cytoskeleton plays a fundamental role in numerous cellular processes, such as cell motility, cytokinesis, and adhesion to the extracellular matrix. Revealing the polarity of individual ...The actin cytoskeleton plays a fundamental role in numerous cellular processes, such as cell motility, cytokinesis, and adhesion to the extracellular matrix. Revealing the polarity of individual actin filaments in intact cells would foster an unprecedented understanding of cytoskeletal processes and their associated mechanical forces. Cryo-electron tomography provides the means for high-resolution structural imaging of cells. However, the low signal-to-noise ratio of cryo-tomograms obscures the high frequencies, and therefore the polarity of actin filaments cannot be directly measured. Here, we developed a method that enables us to determine the polarity of actin filaments in cellular cryo-tomograms. We applied it to reveal the actin polarity distribution in focal adhesions, and show a linear relation between actin polarity and distance from the apical boundary of the adhesion site.
History
DepositionNov 23, 2020-
Header (metadata) releaseDec 2, 2020-
Map releaseDec 2, 2020-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11976.png

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Map

FileDownload / File: emd_11976.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActin filament structure from focal adhesions of mouse embryonic fibroblasts
Voxel sizeX=Y=Z: 3.443 Å
Density
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.041107148 - 0.07008918
Average (Standard dev.)-2.0875111e-06 (±0.004662283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 495.79202 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.4433.4433.443
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z495.792495.792495.792
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.0410.070-0.000

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Supplemental data

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Sample components

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Entire : Actin filament from focal adhesions of mouse embryonic fibroblasts

EntireName: Actin filament from focal adhesions of mouse embryonic fibroblastsMicrofilament
Components
  • Complex: Actin filament from focal adhesions of mouse embryonic fibroblastsMicrofilament

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Supramolecule #1: Actin filament from focal adhesions of mouse embryonic fibroblasts

SupramoleculeName: Actin filament from focal adhesions of mouse embryonic fibroblasts
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil / Material: GOLD
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 14522
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 1.2 sec. / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 7 / Number images used: 43400
CTF correctionSoftware - Name: TOM Toolbox
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.9 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0.4) / Number subtomograms used: 9931

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