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- EMDB-34254: Dinoroseobacter phage vB_DshS-R4C C5 portal vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-34254
TitleDinoroseobacter phage vB_DshS-R4C C5 portal vertex
Map data
SamplevB_DshS-R4C C5 portal vertex != Dinoroseobacter phage vB_DshS-R4C

vB_DshS-R4C C5 portal vertex

  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)
KeywordsMarine bacteriophage / Cryo-EM / Portal vertex / VIRUS
Biological speciesDinoroseobacter phage vB_DshS-R4C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsHuang Y / Sun H / Wei S / Zheng Q / Li S / Zhang R / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Structure and proposed DNA delivery mechanism of a marine roseophage.
Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng ...Authors: Yang Huang / Hui Sun / Shuzhen Wei / Lanlan Cai / Liqin Liu / Yanan Jiang / Jiabao Xin / Zhenqin Chen / Yuqiong Que / Zhibo Kong / Tingting Li / Hai Yu / Jun Zhang / Ying Gu / Qingbing Zheng / Shaowei Li / Rui Zhang / Ningshao Xia /
Abstract: Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene ...Tailed bacteriophages (order, Caudovirales) account for the majority of all phages. However, the long flexible tail of siphophages hinders comprehensive investigation of the mechanism of viral gene delivery. Here, we report the atomic capsid and in-situ structures of the tail machine of the marine siphophage, vB_DshS-R4C (R4C), which infects Roseobacter. The R4C virion, comprising 12 distinct structural protein components, has a unique five-fold vertex of the icosahedral capsid that allows genome delivery. The specific position and interaction pattern of the tail tube proteins determine the atypical long rigid tail of R4C, and further provide negative charge distribution within the tail tube. A ratchet mechanism assists in DNA transmission, which is initiated by an absorption device that structurally resembles the phage-like particle, RcGTA. Overall, these results provide in-depth knowledge into the intact structure and underlining DNA delivery mechanism for the ecologically important siphophages.
History
DepositionSep 8, 2022-
Header (metadata) releaseJul 12, 2023-
Map releaseJul 12, 2023-
UpdateJul 12, 2023-
Current statusJul 12, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34254.png

Downloads & links

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Map

FileDownload / File: emd_34254.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 400 pix.
= 451.2 Å		1.13 Å/pix.
x 400 pix.
= 451.2 Å		1.13 Å/pix.
x 400 pix.
= 451.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.035510615 - 0.059857924
Average (Standard dev.)-0.0004063359 (±0.005018607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 451.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34254_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_34254_half_map_2.map
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Sample components

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Entire : vB_DshS-R4C C5 portal vertex

EntireName: vB_DshS-R4C C5 portal vertex
Components
  • Virus: Dinoroseobacter phage vB_DshS-R4C (virus)

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Supramolecule #1: Dinoroseobacter phage vB_DshS-R4C

SupramoleculeName: Dinoroseobacter phage vB_DshS-R4C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 2590919 / Sci species name: Dinoroseobacter phage vB_DshS-R4C / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Dinoroseobacter shibae DFL 12 = DSM 16493 (bacteria)

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: trRosetta server
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5844
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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