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- EMDB-12590: Bacteriophage YerA41 head icosahedral reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-12590
TitleBacteriophage YerA41 head icosahedral reconstruction
Map dataUnmasked map
Sample
  • Virus: Myoviridae sp. (virus)
Keywordsbacteriophage / phage / virus / capsid
Biological speciesMyoviridae sp. (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.62 Å
AuthorsGomez-Raya-Vilanova MV / Leskinen K / Bhattacharjee A / Virta P / Rosenqvist P / Smith JLR / Bayfield OW / Homberger C / Kerrinnes T / Voge J ...Gomez-Raya-Vilanova MV / Leskinen K / Bhattacharjee A / Virta P / Rosenqvist P / Smith JLR / Bayfield OW / Homberger C / Kerrinnes T / Voge J / Pajunen MI / Skurnik M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust206377 United Kingdom
CitationJournal: Nucleic Acids Res / Year: 2022
Title: The DNA polymerase of bacteriophage YerA41 replicates its T-modified DNA in a primer-independent manner.
Authors: Miguel V Gomez-Raya-Vilanova / Katarzyna Leskinen / Arnab Bhattacharjee / Pasi Virta / Petja Rosenqvist / Jake L R Smith / Oliver W Bayfield / Christina Homberger / Tobias Kerrinnes / Jörg ...Authors: Miguel V Gomez-Raya-Vilanova / Katarzyna Leskinen / Arnab Bhattacharjee / Pasi Virta / Petja Rosenqvist / Jake L R Smith / Oliver W Bayfield / Christina Homberger / Tobias Kerrinnes / Jörg Vogel / Maria I Pajunen / Mikael Skurnik /
Abstract: Yersinia phage YerA41 is morphologically similar to jumbo bacteriophages. The isolated genomic material of YerA41 could not be digested by restriction enzymes, and used as a template by conventional ...Yersinia phage YerA41 is morphologically similar to jumbo bacteriophages. The isolated genomic material of YerA41 could not be digested by restriction enzymes, and used as a template by conventional DNA polymerases. Nucleoside analysis of the YerA41 genomic material, carried out to find out whether this was due to modified nucleotides, revealed the presence of a ca 1 kDa substitution of thymidine with apparent oligosaccharide character. We identified and purified the phage DNA polymerase (DNAP) that could replicate the YerA41 genomic DNA even without added primers. Cryo-electron microscopy (EM) was used to characterize structural details of the phage particle. The storage capacity of the 131 nm diameter head was calculated to accommodate a significantly longer genome than that of the 145 577 bp genomic DNA of YerA41 determined here. Indeed, cryo-EM revealed, in contrast to the 25 Å in other phages, spacings of 33-36 Å between shells of the genomic material inside YerA41 heads suggesting that the heavily substituted thymidine increases significantly the spacing of the DNA packaged inside the capsid. In conclusion, YerA41 appears to be an unconventional phage that packages thymidine-modified genomic DNA into its capsids along with its own DNAP that has the ability to replicate the genome.
History
DepositionMar 9, 2021-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12590.png

Downloads & links

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Map

FileDownload / File: emd_12590.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnmasked map
Voxel sizeX=Y=Z: 1.507 Å
Density
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.14208007 - 0.062453788
Average (Standard dev.)-0.00010432368 (±0.0061087417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100010001000
Spacing100010001000
CellA=B=C: 1507.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Masked map

Fileemd_12590_additional_1.map
AnnotationMasked 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 : Myoviridae sp.

EntireName: Myoviridae sp. (virus)
Components
  • Virus: Myoviridae sp. (virus)

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Supramolecule #1: Myoviridae sp.

SupramoleculeName: Myoviridae sp. / type: virus / ID: 1 / Parent: 0 / Details: Yersinia Phage YerA41; MW570730 / NCBI-ID: 2202564 / Sci species name: Myoviridae sp. / Sci species strain: Yersinia Phage YerA41 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Yersinia ruckeri (bacteria) / Strain: RS41
Virus shellShell ID: 1 / Name: YerA41-B / Diameter: 1310.0 Å / T number (triangulation number): 28

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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: 7.5
Component:
ConcentrationFormulaName
20.0 mMTris-HClTrisTris
150.0 mMNaClSodium chlorideSodium chloride
10.0 mMMgSO4Magnesium sulfate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 59000
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 1.5 sec. / Average electron dose: 50.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 5.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 2900
FSC plot (resolution estimation)

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