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- EMDB-24596: Cryo-EM reconstruction of Acidianus two-tailed virus, ATV -

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Basic information

Entry
Database: EMDB / ID: EMD-24596
TitleCryo-EM reconstruction of Acidianus two-tailed virus, ATV
Map dataATV
Sample
  • Virus: Acidianus two-tailed virus
Biological speciesAcidianus two-tailed virus
Methodhelical reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsWang F / Cvirkaite-Krupovic V / Krupovic M / Egelman EH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138756 United States
CitationJournal: Cell / Year: 2022
Title: Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome.
Authors: Fengbin Wang / Virginija Cvirkaite-Krupovic / Matthijn Vos / Leticia C Beltran / Mark A B Kreutzberger / Jean-Marie Winter / Zhangli Su / Jun Liu / Stefan Schouten / Mart Krupovic / Edward H Egelman /
Abstract: Spindle- or lemon-shaped viruses infect archaea in diverse environments. Due to the highly pleomorphic nature of these virions, which can be found with cylindrical tails emanating from the spindle- ...Spindle- or lemon-shaped viruses infect archaea in diverse environments. Due to the highly pleomorphic nature of these virions, which can be found with cylindrical tails emanating from the spindle-shaped body, structural studies of these capsids have been challenging. We have determined the atomic structure of the capsid of Sulfolobus monocaudavirus 1, a virus that infects hosts living in nearly boiling acid. A highly hydrophobic protein, likely integrated into the host membrane before the virions assemble, forms 7 strands that slide past each other in both the tails and the spindle body. We observe the discrete steps that occur as the tail tubes expand, and these are due to highly conserved quasiequivalent interactions with neighboring subunits maintained despite significant diameter changes. Our results show how helical assemblies can vary their diameters, becoming nearly spherical to package a larger genome and suggest how all spindle-shaped viruses have evolved from archaeal rod-like viruses.
History
DepositionJul 30, 2021-
Header (metadata) releaseMar 30, 2022-
Map releaseMar 30, 2022-
UpdateApr 27, 2022-
Current statusApr 27, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24596.png

Downloads & links

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Map

FileDownload / File: emd_24596.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationATV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.27018037 - 0.76105255
Average (Standard dev.)0.022086626 (±0.0828814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Acidianus two-tailed virus

EntireName: Acidianus two-tailed virus
Components
  • Virus: Acidianus two-tailed virus

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Supramolecule #1: Acidianus two-tailed virus

SupramoleculeName: Acidianus two-tailed virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 315953 / Sci species name: Acidianus two-tailed virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.08 Å
Applied symmetry - Helical parameters - Δ&Phi: -156 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63560
Final angle assignmentType: NOT APPLICABLE

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