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- EMDB-39421: Electron cryotomography of SARS-CoV-2 active virions -

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Basic information

Entry
Database: EMDB / ID: EMD-39421
TitleElectron cryotomography of SARS-CoV-2 active virions
Map data
Sample
  • Virus: Severe acute respiratory syndrome coronavirus 2
Keywordsvirions / spike protein / VIRUS
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodelectron tomography / cryo EM / Resolution: 7.53 Å
AuthorsDokainish HM / Maenaka K
Funding support Japan, 8 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101093 Japan
Japan Agency for Medical Research and Development (AMED)JP20ae0101047 Japan
Japan Agency for Medical Research and Development (AMED)JP21fk0108463 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121037 Japan
Japan Agency for Medical Research and Development (AMED)JP223fa627005 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
Japan Science and TechnologyJPMJCR20H8 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP20H05873 Japan
CitationJournal: To Be Published
Title: Unprecedented spike flexibility revealed by BSL3 Cryo-ET of active SARS-CoV-2 virions
Authors: Dokainish HM / Fukuhara H / Maenaka K
History
DepositionMar 11, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39421.png

Downloads & links

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Map

FileDownload / File: emd_39421.map.gz / Format: CCP4 / Size: 636 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
7.53 Å/pix.
x 318 pix.
= 2395.812 Å		7.53 Å/pix.
x 1024 pix.
= 7714.816 Å		7.53 Å/pix.
x 1024 pix.
= 7714.816 Å

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Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 7.534 Å
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Minimum - Maximum-877.0 - 707.0
Average (Standard dev.)150.223559999999992 (±37.28454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-15900
Dimensions10241024318
Spacing10241024318
CellA: 7714.816 Å / B: 7714.816 Å / C: 2395.812 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39421_additional_1.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 / 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: VeroE6/TMPRSS2

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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 / Details: Opti-MEM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 291 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 0.73 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.2 µm / Nominal defocus min: 0.2 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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.53 Å / Software - Name: IMOD (ver. 12.35) / Number images used: 121
CTF correctionSoftware - Name: IMOD (ver. 12.35) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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