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- EMDB-33149: SSV19 -

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Basic information

Entry
Database: EMDB / ID: EMD-33149
TitleSSV19
Map data
Sample
  • Virus: Sulfolobus spindle-shaped virus
Biological speciesSulfolobus spindle-shaped virus
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsLiu HR / Chen WY
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)31970170 China
National Natural Science Foundation of China (NSFC)91951000 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural insights into a spindle-shaped archaeal virus with a sevenfold symmetrical tail.
Authors: Zhen Han / Wanjuan Yuan / Hao Xiao / Li Wang / Junxia Zhang / Yuning Peng / Lingpeng Cheng / Hongrong Liu / Li Huang /
Abstract: Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have ...Archaeal viruses with a spindle-shaped virion are abundant and widespread in extremely diverse environments. However, efforts to obtain the high-resolution structure of a spindle-shaped virus have been unsuccessful. Here, we present the structure of SSV19, a spindle-shaped virus infecting the hyperthermophilic archaeon sp. E11-6. Our near-atomic structure reveals an unusual sevenfold symmetrical virus tail consisting of the tailspike, nozzle, and adaptor proteins. The spindle-shaped capsid shell is formed by seven left-handed helical strands, constructed of the hydrophobic major capsid protein, emanating from the highly glycosylated tail assembly. Sliding between adjacent strands is responsible for the variation of a virion in size. Ultrathin sections of the SSV19-infected cells show that SSV19 virions adsorb to the host cell membrane through the tail after penetrating the S-layer. The tailspike harbors a putative endo-mannanase domain, which shares structural similarity to a endo-mannanase. Molecules of glycerol dibiphytanyl glycerol tetraether lipid were observed in hydrophobic clefts between the tail and the capsid shell. The nozzle protein resembles the stem and clip domains of the portals of herpesviruses and bacteriophages, implying an evolutionary relationship among the archaeal, bacterial, and eukaryotic viruses.
History
DepositionMar 27, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33149.png

Downloads & links

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Map

FileDownload / File: emd_33149.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 2.54 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.026854029 - 0.059751134
Average (Standard dev.)-9.186331e-05 (±0.0041438956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1300.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Sulfolobus spindle-shaped virus

EntireName: Sulfolobus spindle-shaped virus
Components
  • Virus: Sulfolobus spindle-shaped virus

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Supramolecule #1: Sulfolobus spindle-shaped virus

SupramoleculeName: Sulfolobus spindle-shaped virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2491899 / Sci species name: Sulfolobus spindle-shaped virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109865

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