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- EMDB-35876: Cellular components at INS-1E cell interior under basal condition -

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Basic information

Entry
Database: EMDB / ID: EMD-35876
TitleCellular components at INS-1E cell interior under basal condition
Map data
Sample
  • Cell: INS-1E
Keywordsinsulin secretion / cytoskeleton / CYTOSOLIC PROTEIN
Biological speciesRattus (rat)
Methodelectron tomography / cryo EM
AuthorsLi W / Li A / Yu B / Zhang X / Liu X / White K / Stevens R / Baumeister W / Sali A / Jasnin M / Sun L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography.
Authors: Weimin Li / Angdi Li / Bing Yu / Xiaoxiao Zhang / Xiaoyan Liu / Kate L White / Raymond C Stevens / Wolfgang Baumeister / Andrej Sali / Marion Jasnin / Liping Sun /
Abstract: Actin mediates insulin secretion in pancreatic β-cells through remodeling. Hampered by limited resolution, previous studies have offered an ambiguous depiction as depolymerization and ...Actin mediates insulin secretion in pancreatic β-cells through remodeling. Hampered by limited resolution, previous studies have offered an ambiguous depiction as depolymerization and repolymerization. We report the in situ structure of actin remodeling in INS-1E β-cells during glucose-stimulated insulin secretion at nanoscale resolution. After remodeling, the actin filament network at the cell periphery exhibits three marked differences: 12% of actin filaments reorient quasi-orthogonally to the ventral membrane; the filament network mainly remains as cell-stabilizing bundles but partially reconfigures into a less compact arrangement; actin filaments anchored to the ventral membrane reorganize from a "netlike" to a "blooming" architecture. Furthermore, the density of actin filaments and microtubules around insulin secretory granules decreases, while actin filaments and microtubules become more densely packed. The actin filament network after remodeling potentially precedes the transport and release of insulin secretory granules. These findings advance our understanding of actin remodeling and its role in glucose-stimulated insulin secretion.
History
DepositionApr 9, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35876.png

Downloads & links

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Map

FileDownload / File: emd_35876.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.11 Å/pix.
x 271 pix.
= 3282.352 Å		12.11 Å/pix.
x 1024 pix.
= 12402.688 Å		12.11 Å/pix.
x 1024 pix.
= 12402.688 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 12.112 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.59643567 - 0.28225017
Average (Standard dev.)-0.0022096576 (±0.027034493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10241024271
Spacing10241024271
CellA: 12402.688 Å / B: 12402.688 Å / C: 3282.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : INS-1E

EntireName: INS-1E
Components
  • Cell: INS-1E

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Supramolecule #1: INS-1E

SupramoleculeName: INS-1E / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Rattus (rat)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.45
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.5 / Focused ion beam - Duration: 30 / Focused ion beam - Temperature: 78 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 250
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm

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Image processing

Final reconstructionNumber images used: 61

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