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- PDB-8gtc: Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail... -

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Basic information

Entry
Database: PDB / ID: 8gtc
TitleCryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex
Components
  • Distal tail protein
  • Hub protein
  • Major tail protein
  • Megatron protein
  • Ribonuclease III
KeywordsVIRAL PROTEIN / Marine bacteriophage / Cryo-EM / Siphophage / Baseplate / Megatron protein / Tail fibre protein / Distal tail protein / Hub protein
Function / homology
Function and homology information


Protein of unknown function DUF2793 / Protein of unknown function (DUF2793) / GTA TIM-barrel-like domain / : / GTA TIM-barrel-like domain / Rcc01698-like, C-terminal / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Baseplate hub protein, N-terminal attachment domain / Bacteriophage phiJL001, Gp84 ...Protein of unknown function DUF2793 / Protein of unknown function (DUF2793) / GTA TIM-barrel-like domain / : / GTA TIM-barrel-like domain / Rcc01698-like, C-terminal / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Baseplate hub protein, N-terminal attachment domain / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Tip attachment protein J / Putative phage tail protein / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Gene transfer agent / Ribonuclease III / Tail protein / Tail protein / Major tail protein
Similarity search - Component
Biological speciesDinoroseobacter phage vB_DshS-R4C (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 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

Downloads & links

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Assembly

Deposited unit
A: Major tail protein
B: Major tail protein
C: Major tail protein
D: Major tail protein
E: Major tail protein
F: Major tail protein
G: Distal tail protein
H: Distal tail protein
I: Distal tail protein
J: Distal tail protein
K: Distal tail protein
L: Distal tail protein
M: Megatron protein
N: Megatron protein
O: Megatron protein
P: Hub protein
Q: Hub protein
R: Hub protein
S: Ribonuclease III
T: Ribonuclease III
U: Ribonuclease III
V: Ribonuclease III
W: Ribonuclease III
X: Ribonuclease III
Y: Ribonuclease III
Z: Ribonuclease III
a: Ribonuclease III


Theoretical massNumber of molelcules
Total (without water)983,64627
Polymers983,64627
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
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
#2: Protein
Distal tail protein


Mass: 23378.309 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E7X5
#3: Protein Megatron protein


Mass: 154569.125 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E933
#4: Protein Hub protein


Mass: 31055.357 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E762
#5: Protein
Ribonuclease III


Mass: 22783.799 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Dinoroseobacter phage vB_DshS-R4C (virus) / References: UniProt: A0A4Y6E764

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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: C3 (3 fold cyclic)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11598 / Symmetry type: POINT

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