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- PDB-8gtf: Cryo-EM model of the marine siphophage vB_DshS-R4C stopper-termin... -

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Basic information

Entry
Database: PDB / ID: 8gtf
TitleCryo-EM model of the marine siphophage vB_DshS-R4C stopper-terminator complex
Components
  • Head-to-tail joining protein
  • Major tail protein
  • Terminator protein
KeywordsVIRUS / Marine bacteriophage / Cryo-EM / Siphophage / Stopper protein / Terminator protein / Head-to-tail interface
Function / homologyBacteriophage tail attachment protein FII / : / Phage Head-Tail Attachment protein / virion assembly / Head-to-tail joining protein / Minor tail protein / Major tail protein
Function and homology information
Biological speciesDinoroseobacter phage vB_DshS-R4C (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsHuang, Y. / Sun, H. / Wei, S. / Zheng, Q. / Li, S. / Zhang, R. / Xia, N.
Funding support1items
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, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Head-to-tail joining protein
N: Head-to-tail joining protein
O: Head-to-tail joining protein
P: Head-to-tail joining protein
Q: Head-to-tail joining protein
X: Head-to-tail joining protein
e: Major tail protein
f: Major tail protein
g: Major tail protein
h: Major tail protein
i: Major tail protein
j: Major tail protein
k: Terminator protein
l: Terminator protein
m: Terminator protein
n: Terminator protein
o: Terminator protein
p: Terminator protein


Theoretical massNumber of molelcules
Total (without water)236,32818
Polymers236,32818
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Head-to-tail joining protein


Mass: 10946.397 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E757
#2: Protein
Major tail protein


Mass: 13574.816 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6EGR9
#3: Protein
Terminator protein


Mass: 14866.825 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E8T3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dinoroseobacter phage vB_DshS-R4C / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Dinoroseobacter phage vB_DshS-R4C (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Dinoroseobacter shibae DFL 12 = DSM 16493
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5844 / Symmetry type: POINT

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