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- EMDB-65324: SARS-CoV-2 Ancestral strain spike S-6P -

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Basic information

Entry
Database: EMDB / ID: EMD-65324
TitleSARS-CoV-2 Ancestral strain spike S-6P
Map data
Sample
  • Complex: SARS-CoV-2 spike glycoprotein Ancestral S-6P
KeywordsSARS-CoV-2 spike protein / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsHemmi T / Yajima H / Hashiguchi T
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23KJ1304 Japan
CitationJournal: To Be Published
Title: SARS-CoV-2 Ancestral strain spike S-6P
Authors: Hemmi T / Yajima H / Hashiguchi T
History
DepositionJul 10, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65324.png

Downloads & links

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Map

FileDownload / File: emd_65324.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 355.2 Å		0.93 Å/pix.
x 384 pix.
= 355.2 Å		0.93 Å/pix.
x 384 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.925 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0725
Minimum - Maximum-0.22377922 - 0.528939
Average (Standard dev.)0.00044555773 (±0.012471198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65324_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_65324_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65324_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 spike glycoprotein Ancestral S-6P

EntireName: SARS-CoV-2 spike glycoprotein Ancestral S-6P
Components
  • Complex: SARS-CoV-2 spike glycoprotein Ancestral S-6P

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Supramolecule #1: SARS-CoV-2 spike glycoprotein Ancestral S-6P

SupramoleculeName: SARS-CoV-2 spike glycoprotein Ancestral S-6P / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 185895
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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