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- EMDB-62342: The DNA coil forming by the nucleoprotein filaments in SEV1 -

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Basic information

Entry
Database: EMDB / ID: EMD-62342
TitleThe DNA coil forming by the nucleoprotein filaments in SEV1
Map data
Sample
  • Virus: Sulfolobus ellipsoid virus 1
Keywordsnucleocapsid protein / VIRUS
Biological speciesSulfolobus ellipsoid virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 24.7 Å
AuthorsZhang H / Wang H / Zhu P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)E2VK311RA1 China
CitationJournal: To Be Published
Title: Insights into the spool-like architecture and infection strategy of the archaeal virus SEV1
Authors: Zhang H / Wang H / Zhu P
History
DepositionNov 10, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62342.png

Downloads & links

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Map

FileDownload / File: emd_62342.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.44 Å/pix.
x 100 pix.
= 544. Å		5.44 Å/pix.
x 100 pix.
= 544. Å		5.44 Å/pix.
x 100 pix.
= 544. Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.44 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.99
Minimum - Maximum-1.3355893 - 2.0955777
Average (Standard dev.)0.058554273 (±0.2733493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62342_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_62342_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62342_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sulfolobus ellipsoid virus 1

EntireName: Sulfolobus ellipsoid virus 1
Components
  • Virus: Sulfolobus ellipsoid virus 1

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Supramolecule #1: Sulfolobus ellipsoid virus 1

SupramoleculeName: Sulfolobus ellipsoid virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2056194 / Sci species name: Sulfolobus ellipsoid virus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No

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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: 3.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
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: 24.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 231
ExtractionNumber tomograms: 68 / Number images used: 1796
Final angle assignmentType: MAXIMUM LIKELIHOOD

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