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- EMDB-15045: Localized reconstruction of bacteriophage phiCjT23 major capsid p... -

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Basic information

Entry
Database: EMDB / ID: EMD-15045
TitleLocalized reconstruction of bacteriophage phiCjT23 major capsid protein trimer type 2
Map data
Sample
  • Virus: unidentified (others)
    • Protein or peptide: Major capsid protein P5
Keywordsbacteriophage / phiCjT23 / VIRUS
Biological speciesFlavobacterium phage (virus) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKejzar N / Abrishami V / Selvaraj M / Huiskonen JT
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution.
Authors: Nejc Kejzar / Elina Laanto / Ilona Rissanen / Vahid Abrishami / Muniyandi Selvaraj / Sylvain Moineau / Janne Ravantti / Lotta-Riina Sundberg / Juha T Huiskonen /
Abstract: The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid ...The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution.
History
DepositionMay 26, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15045.png

Downloads & links

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Map

FileDownload / File: emd_15045.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 200 pix.
= 248. Å		1.24 Å/pix.
x 200 pix.
= 248. Å		1.24 Å/pix.
x 200 pix.
= 248. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.19527903 - 0.30766833
Average (Standard dev.)0.00073426415 (±0.017466163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 248.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15045_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_15045_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15045_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : unidentified

EntireName: unidentified (others)
Components
  • Virus: unidentified (others)
    • Protein or peptide: Major capsid protein P5

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Supramolecule #1: unidentified

SupramoleculeName: unidentified / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 32644 / Sci species name: unidentified / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 600.0 Å / T number (triangulation number): 21

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Macromolecule #1: Major capsid protein P5

MacromoleculeName: Major capsid protein P5 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium phage (virus)
Molecular weightTheoretical: 26.180783 KDa
SequenceString: MKIATITGVT KSPELQVTKA IGALILSSDV ALSALTTEKI SIYIERGNGS NVILANKVLL KDFILASTYG TENTQSDADN AMIALCELA DEGSIYLADK ESIKITLEDL ISDKRYDLHG IEEPQQTNNL FFFEQKSVAS EEFNKKIDVQ GFDLAIMTVD D SVSDLSYQ ...String:
MKIATITGVT KSPELQVTKA IGALILSSDV ALSALTTEKI SIYIERGNGS NVILANKVLL KDFILASTYG TENTQSDADN AMIALCELA DEGSIYLADK ESIKITLEDL ISDKRYDLHG IEEPQQTNNL FFFEQKSVAS EEFNKKIDVQ GFDLAIMTVD D SVSDLSYQ YSNGQVVKYL PFELQTLSRD IDPIQAVLSD GKVVQGLTDR LTLPLVAVVG IEINKSQGSI INFVVRCLKT V

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Localized reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 257197
Initial angle assignmentType: OTHER / Details: Localized reconstruction
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8a02:
Bacteriophage phiCjT23 major capsid protein trimer type 2

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