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- EMDB-15051: Localized reconstruction of flavobacterium infecting lipid-contai... -

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Basic information

Entry
Database: EMDB / ID: EMD-15051
TitleLocalized reconstruction of flavobacterium infecting lipid-containing phage FLiP vertex
Map data
Sample
  • Virus: Flavobacterium phage FLiP (virus)
    • Protein or peptide: Penton protein P12
Keywordsbacteriophage / Flavobacterium / lipid-containing / phage / FLiP / penton protein / VIRUS
Function / homologyUncharacterized protein
Function and homology information
Biological speciesFlavobacterium phage FLiP (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsKejzar N / Abrishami V / Selvaraj M / Huiskonen JT
Funding support1 items
OrganizationGrant numberCountry
Not funded
Citation
Journal: 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.
#1: Journal: Proc Natl Acad Sci U S A / Year: 2017
Title: Virus found in a boreal lake links ssDNA and dsDNA viruses.
Authors: Laanto E / Mantynen S / De Colibus L / Marjakangas J / Gillum A / Stuart DI / Ravantti JJ / Huiskonen JT / Sundberg LR
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_15051.png

Downloads & links

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Map

FileDownload / File: emd_15051.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 200 pix.
= 270. Å		1.35 Å/pix.
x 200 pix.
= 270. Å		1.35 Å/pix.
x 200 pix.
= 270. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.06704435 - 0.113037385
Average (Standard dev.)0.00080474635 (±0.009176662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15051_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #1

Fileemd_15051_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15051_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Flavobacterium phage FLiP

EntireName: Flavobacterium phage FLiP (virus)
Components
  • Virus: Flavobacterium phage FLiP (virus)
    • Protein or peptide: Penton protein P12

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Supramolecule #1: Flavobacterium phage FLiP

SupramoleculeName: Flavobacterium phage FLiP / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2023716 / Sci species name: Flavobacterium phage FLiP / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Flavobacterium (bacteria)

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Macromolecule #1: Penton protein P12

MacromoleculeName: Penton protein P12 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium phage FLiP (virus)
Molecular weightTheoretical: 16.851057 KDa
SequenceString:
DFSTIPIDYV KAKDPNTIDF CLSYLELYHT TKAVKACTPF SFILGSDAGM QRATETTESL YWGKVILDIN PNLSPLVNTT IVLEIESML SSNSINRSEN KRITRYIEKE NFVNESSERF EFFKSMELSH LSTAYDVYVT FIGFKIDL

UniProtKB: Uncharacterized protein

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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 POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 22.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Localized reconstruction
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28212
Initial angle assignmentType: OTHER / Details: Localized reconstruction
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8a06:
Flavobacterium infecting lipid-containing phage FLiP penton protein

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