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- EMDB-4797: In situ subtomogram average of 80S ribosome from Dictyostelium di... -

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Basic information

Entry
Database: EMDB / ID: EMD-4797
TitleIn situ subtomogram average of 80S ribosome from Dictyostelium discoideum
Map dataIn situ subtomogram average of 80S ribosome from Dictyostelium discoideum
Sample
  • Complex: 80S ribosome within the native cellular environment of Dictyostelium discoideum
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 26.0 Å
AuthorsJasnin M / Fukuda Y / Beck F
Funding support1 items
OrganizationGrant numberCountry
Human Frontier Science ProgramRGP0035/2016
CitationJournal: Structure / Year: 2019
Title: The Architecture of Traveling Actin Waves Revealed by Cryo-Electron Tomography.
Authors: Marion Jasnin / Florian Beck / Mary Ecke / Yoshiyuki Fukuda / Antonio Martinez-Sanchez / Wolfgang Baumeister / Günther Gerisch /
Abstract: Actin waves are dynamic supramolecular structures involved in cell migration, cytokinesis, adhesion, and neurogenesis. Although wave-like propagation of actin networks is a widespread phenomenon, the ...Actin waves are dynamic supramolecular structures involved in cell migration, cytokinesis, adhesion, and neurogenesis. Although wave-like propagation of actin networks is a widespread phenomenon, the actin architecture underlying wave propagation remained unknown. In situ cryo-electron tomography of Dictyostelium cells unveils the wave architecture and provides evidence for wave progression by de novo actin nucleation. Subtomogram averaging reveals the structure of Arp2/3 complex-mediated branch junctions in their native state, and enables quantitative analysis of the 3D organization of branching within the waves. We find an excess of branches directed toward the substrate-attached membrane, and tent-like structures at sites of branch clustering. Fluorescence imaging shows that Arp2/3 clusters follow accumulation of the elongation factor VASP. We propose that filament growth toward the membrane lifts up the actin network as the wave propagates, until depolymerization of oblique filaments at the back causes the collapse of horizontal filaments into a compact layer.
History
DepositionApr 10, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseJul 3, 2019-
UpdateAug 21, 2019-
Current statusAug 21, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4797.png

Downloads & links

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Map

FileDownload / File: emd_4797.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ subtomogram average of 80S ribosome from Dictyostelium discoideum
Voxel sizeX=Y=Z: 4.21 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.054659568 - 0.13687168
Average (Standard dev.)0.0010425029 (±0.028563475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 421.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.214.214.21
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z421.000421.000421.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0550.1370.001

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Supplemental data

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Sample components

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Entire : 80S ribosome within the native cellular environment of Dictyostel...

EntireName: 80S ribosome within the native cellular environment of Dictyostelium discoideum
Components
  • Complex: 80S ribosome within the native cellular environment of Dictyostelium discoideum

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Supramolecule #1: 80S ribosome within the native cellular environment of Dictyostel...

SupramoleculeName: 80S ribosome within the native cellular environment of Dictyostelium discoideum
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote) / Location in cell: actin waves

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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: 6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.0 µm / Calibrated defocus min: 0.0 µm / Calibrated magnification: 33000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
DetailsIn-focus Volta Phase plate imaging
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 12 / Number images used: 9692
CTF correctionDetails: In-focus Volta phase plate imaging
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PyTom / Number subtomograms used: 3934

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