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- EMDB-24587: Cryo-EM reconstruction of Sulfolobus monocaudavirus SMV1, symmetry 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-24587
TitleCryo-EM reconstruction of Sulfolobus monocaudavirus SMV1, symmetry 3
Map datasym3
Sample
  • Virus: Sulfolobus monocaudavirus SMV1
    • Protein or peptide: major capsid protein
Keywordshelical symmetry / archaeal virus / lemon-shaped virus / spindle-shaped virus / VIRUS
Function / homologymembrane / Hypothetical membrane protein
Function and homology information
Biological speciesSulfolobus monocaudavirus SMV1
Methodhelical reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsWang F / Cvirkaite-Krupovic V
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-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24587.png

Downloads & links

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Map

FileDownload / File: emd_24587.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsym3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 448 pix.
= 492.8 Å		1.1 Å/pix.
x 448 pix.
= 492.8 Å		1.1 Å/pix.
x 448 pix.
= 492.8 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: 0.35
Minimum - Maximum-0.33918878 - 1.0857999
Average (Standard dev.)0.02718416 (±0.10318133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 492.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Sulfolobus monocaudavirus SMV1

EntireName: Sulfolobus monocaudavirus SMV1
Components
  • Virus: Sulfolobus monocaudavirus SMV1
    • Protein or peptide: major capsid protein

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Supramolecule #1: Sulfolobus monocaudavirus SMV1

SupramoleculeName: Sulfolobus monocaudavirus SMV1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1351702 / Sci species name: Sulfolobus monocaudavirus SMV1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: major capsid protein

MacromoleculeName: major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sulfolobus monocaudavirus SMV1
Molecular weightTheoretical: 16.179297 KDa
SequenceString:
MSVSVVVPSA KATGAGGKKA KTFKVIKVST PKVNNVHVPK IKKATRIHDP GAISGSLAKV TFGTNGFDIP TIAIALLIVG VIIGLSGLI LSIFATATAS AISNPSPGTL AYNLTHPLIN GMVSFFSFFP TLYVLLGVTG IVLIAAGIIS IIMEKFKT

UniProtKB: Hypothetical membrane protein

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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: 0.7 Å
Applied symmetry - Helical parameters - Δ&Phi: -155.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 59521
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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