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- EMDB-18615: Cryo-electron tomogram of small unilamellar vesicles decorated wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-18615
TitleCryo-electron tomogram of small unilamellar vesicles decorated with poliovirus protein 2C
Map dataCryo-electron tomogram of small unilamellar vesicles decorated with the poliovirus protein 2C
Sample
  • Complex: Poliovirus protein 2C bound to small unilamellar vesicles
Keywordsenterovirus / protein-membrane interaction / AAA+ ATPase / 2C / VIRAL PROTEIN
Biological speciesHuman poliovirus 1 Mahoney
Methodelectron tomography / cryo EM
AuthorsShankar K / Dahmane S / Carlson LA
Funding support Sweden, European Union, France, 4 items
OrganizationGrant numberCountry
Swedish Research Council2018-05851 Sweden
Swedish Research Council2021-01145 Sweden
European Commission101033469European Union
Human Frontier Science Program (HFSP)CDA00047/2017 C France
CitationJournal: To Be Published
Title: In vitro reconstitution reveals membrane clustering and double-stranded RNA recruitment by the enteroviral AAA+ ATPase 2C
Authors: Shankar K / Dahmane S / Carlson LA
History
DepositionOct 8, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18615.png

Downloads & links

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Map

FileDownload / File: emd_18615.map.gz / Format: CCP4 / Size: 477.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of small unilamellar vesicles decorated with the poliovirus protein 2C
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.26 Å/pix.
x 109 pix.
= 1554.34 Å		14.26 Å/pix.
x 1052 pix.
= 15001.521 Å		14.26 Å/pix.
x 1091 pix.
= 15557.66 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: 14.26 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3897.389000000000124 - 4091.043999999999869
Average (Standard dev.)95.041259999999994 (±358.804779999999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin10491-59
Dimensions10521091109
Spacing10911052109
CellA: 15557.66 Å / B: 15001.5205 Å / C: 1554.34 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: IsoNet-denoised version of the tomogram

Fileemd_18615_additional_1.map
AnnotationIsoNet-denoised version of the tomogram
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Poliovirus protein 2C bound to small unilamellar vesicles

EntireName: Poliovirus protein 2C bound to small unilamellar vesicles
Components
  • Complex: Poliovirus protein 2C bound to small unilamellar vesicles

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Supramolecule #1: Poliovirus protein 2C bound to small unilamellar vesicles

SupramoleculeName: Poliovirus protein 2C bound to small unilamellar vesicles
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 38 kDa/nm

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 43

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