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- EMDB-15185: Prefusion spike of SARS-CoV-2 (Wuhan), 1-RBD-up conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-15185
TitlePrefusion spike of SARS-CoV-2 (Wuhan), 1-RBD-up conformation
Map data
Sample
  • Virus: Severe acute respiratory syndrome coronavirus 2
Keywordsspike / SARS-CoV-2 / rbd up / receptor binding / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 27.75 Å
AuthorsCalder LJ / Calcraft T / Hussain S / Harvey R / Rosenthal PB
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001143 United Kingdom
Cancer Research UKFC001143 United Kingdom
CitationJournal: Commun Biol / Year: 2022
Title: Electron cryotomography of SARS-CoV-2 virions reveals cylinder-shaped particles with a double layer RNP assembly.
Authors: Lesley J Calder / Thomas Calcraft / Saira Hussain / Ruth Harvey / Peter B Rosenthal /
Abstract: SARS-CoV-2 is a lipid-enveloped Betacoronavirus and cause of the Covid-19 pandemic. To study the three-dimensional architecture of the virus, we perform electron cryotomography (cryo-ET) on SARS-Cov- ...SARS-CoV-2 is a lipid-enveloped Betacoronavirus and cause of the Covid-19 pandemic. To study the three-dimensional architecture of the virus, we perform electron cryotomography (cryo-ET) on SARS-Cov-2 virions and three variants revealing particles of regular cylindrical morphology. The ribonucleoprotein particles packaging the genome in the virion interior form a dense, double layer assembly with a cylindrical shape related to the overall particle morphology. This organisation suggests structural interactions important to virus assembly.
History
DepositionJun 15, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15185.png

Downloads & links

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Map

FileDownload / File: emd_15185.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
4.44 Å/pix.
x 100 pix.
= 444. Å		4.44 Å/pix.
x 100 pix.
= 444. Å		4.44 Å/pix.
x 100 pix.
= 444. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.44 Å
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Contour LevelBy AUTHOR: 0.0515
Minimum - Maximum-0.1923632 - 0.3236154
Average (Standard dev.)0.00009016377 (±0.014607984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15185_msk_1.map
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Half map: #1

Fileemd_15185_half_map_1.map
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Half map: #2

Fileemd_15185_half_map_2.map
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Sample components

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Entire : Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2
Components
  • Virus: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / Details: Virus grown in Vero V1 cells and purified / NCBI-ID: 2697049
Sci species name: Severe acute respiratory syndrome coronavirus 2
Sci species strain: Wuhan / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum ER / Energy filter - Slit width: 20 eV
DetailsTilt series collected using dose symmetric scheme.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-4 / Average exposure time: 1.7 sec. / Average electron dose: 2.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 64000
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 27.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 474
ExtractionNumber tomograms: 18 / Number images used: 4418
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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