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- EMDB-13585: Cryo-electron tomography of ASC signalling sites in pyroptotic cells -

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Basic information

Entry
Database: EMDB / ID: EMD-13585
TitleCryo-electron tomography of ASC signalling sites in pyroptotic cells
Map data
Sample
  • Cell: FIB milled iBMDMs
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsLiu Y / Zhai H / Alemayehu H / Hopkins LJ / Borgeaud AC / Heroven C / Howe JD / Boulanger J / Bryant CE / Modis Y
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: Cryo-electron tomography of ASC signalling sites in pyroptotic cells
Authors: Liu Y / Zhai H / Alemayehu H / Hopkins LJ / Borgeaud AC / Heroven C / Howe JD / Boulanger J / Bryant CE / Modis Y
History
DepositionSep 16, 2021-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13585.png

Downloads & links

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Map

FileDownload / File: emd_13585.map.gz / Format: CCP4 / Size: 760.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 13.58 Å
Density
Minimum - Maximum-40.850227 - 37.43507
Average (Standard dev.)0.0003896798 (±5.07909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin005
Dimensions13151024148
Spacing10241315148
CellA: 13905.92 Å / B: 17857.7 Å / C: 2009.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : FIB milled iBMDMs

EntireName: FIB milled iBMDMs
Components
  • Cell: FIB milled iBMDMs

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Supramolecule #1: FIB milled iBMDMs

SupramoleculeName: FIB milled iBMDMs / 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
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
Details: DMEM medium supplemented with 10% heat-inactivated FBS (Gibco)
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: LEICA EM GP
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 1 nA / Focused ion beam - Duration: 1500 sec. / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 10000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: Lamella were made using a Scios DualBeam FIB/SEM (FEI) equipped with a Quorum cryo-stage (PP3010T). Rough milling was performed using 0.5 to 0.1 nA current. Fine milling ...Focused ion beam - Details: Lamella were made using a Scios DualBeam FIB/SEM (FEI) equipped with a Quorum cryo-stage (PP3010T). Rough milling was performed using 0.5 to 0.1 nA current. Fine milling was done using 50 to 10 pA current..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 121 / Average electron dose: 1.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 7.0 µm / Nominal defocus min: 4.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution method: OTHER / Software - Name: eTomo / Number images used: 100
CTF correctionSoftware - Name: eTomo (ver. 4.10.20)

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