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- EMDB-4790: In situ subtomogram average of Arp2/3 complex-mediated branch jun... -

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Basic information

Entry
Database: EMDB / ID: EMD-4790
TitleIn situ subtomogram average of Arp2/3 complex-mediated branch junctions from Dictyostelium discoideum
Map dataActin filament branch junction associated with the Arp2/3 complex
Sample
  • Organelle or cellular component: Actin filament branch junction associated with the Arp2/3 complex within the native cellular environment of Dictyostelium discoideum
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 32.0 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: 0.0618
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0618
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4790.png

Downloads & links

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Map

FileDownload / File: emd_4790.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationActin filament branch junction associated with the Arp2/3 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.21 Å/pix.
x 160 pix.
= 673.6 Å		4.21 Å/pix.
x 160 pix.
= 673.6 Å		4.21 Å/pix.
x 160 pix.
= 673.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0618 / Movie #1: 0.0618
Minimum - Maximum-0.045148995 - 0.14135109
Average (Standard dev.)0.00078801595 (±0.011738094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 673.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.214.214.21
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z673.600673.600673.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0450.1410.001

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Supplemental data

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Sample components

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Entire : Actin filament branch junction associated with the Arp2/3 complex...

EntireName: Actin filament branch junction associated with the Arp2/3 complex within the native cellular environment of Dictyostelium discoideum
Components
  • Organelle or cellular component: Actin filament branch junction associated with the Arp2/3 complex within the native cellular environment of Dictyostelium discoideum

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Supramolecule #1: Actin filament branch junction associated with the Arp2/3 complex...

SupramoleculeName: Actin filament branch junction associated with the Arp2/3 complex within the native cellular environment of Dictyostelium discoideum
type: organelle_or_cellular_component / 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
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
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 FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 32.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PyTom / Number subtomograms used: 1583
ExtractionNumber tomograms: 19 / Number images used: 4372
CTF correctionDetails: In-focus Volta phase plate imaging
Final angle assignmentType: NOT APPLICABLE

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