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- EMDB-62178: The average map of six beads composed of the nucleocapsid protein... -

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Basic information

Entry
Database: EMDB / ID: EMD-62178
TitleThe average map of six beads composed of the nucleocapsid protein from SEV1
Map data
Sample
  • Virus: Sulfolobus ellipsoid virus 1
Keywordsnucleocapsid protein / VIRUS
Biological speciesSulfolobus ellipsoid virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 18.1 Å
AuthorsZhang H / Wang H / Zhu P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)E2VK311RA1 China
CitationJournal: Sci Adv / Year: 2025
Title: Insights into the spool-like architecture and infection strategy of an enveloped archaeal virus.
Authors: Haonan Zhang / Haina Wang / Yan Li / Yunxuan Fan / Zhenfeng Zhang / Hongyu Chen / Kai Song / Li Huang / Ping Zhu /
Abstract: Archaeal viruses are well known for their diverse morphologies and extreme stability. Here, we used cryo-electron tomography to analyze the structure of ellipsoid virus 1 (SEV1), an archaeal virus ...Archaeal viruses are well known for their diverse morphologies and extreme stability. Here, we used cryo-electron tomography to analyze the structure of ellipsoid virus 1 (SEV1), an archaeal virus with an ellipsoidal shape and a lipid envelope, and its infection strategy. We show that the SEV1 nucleocapsid adopts a "coil-stacking" architecture with substantial flexibility. The major capsid protein VP4, whose homologs are widespread in the thermoacidic environments around the Pacific Rim, binds genomic DNA in the formation of a nucleoprotein filament with a "beads-on-a-string" appearance. The virion is notably stable at high temperature and acidic pH, and the envelope of SEV1 is crucial to the thermostability of the virion. The infected cell undergoes cytoplasmic condensation to form patches associated with the assembly intermediates of the progeny virions. The nascent virions are released through virus-associated pyramids (VAPs), which are constructed of an SEV1 protein distinctly different at the amino acid sequence level from other known VAP proteins.
History
DepositionOct 24, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62178.png

Downloads & links

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Map

FileDownload / File: emd_62178.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 60 pix.
= 163.2 Å		2.72 Å/pix.
x 60 pix.
= 163.2 Å		2.72 Å/pix.
x 60 pix.
= 163.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.7771773 - 0.7211996
Average (Standard dev.)0.0028411585 (±0.18688414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 163.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_62178_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62178_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_62178_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 : 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: 18.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 220
ExtractionNumber tomograms: 68 / Number images used: 300
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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