8GTC | pdb_00008gtc

Cryo-EM model of the marine siphophage vB_DshS-R4C baseplate-tail complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and proposed DNA delivery mechanism of a marine roseophage.

Huang, Y.Sun, H.Wei, S.Cai, L.Liu, L.Jiang, Y.Xin, J.Chen, Z.Que, Y.Kong, Z.Li, T.Yu, H.Zhang, J.Gu, Y.Zheng, Q.Li, S.Zhang, R.Xia, N.

(2023) Nat Commun 14: 3609-3609

  • DOI: https://doi.org/10.1038/s41467-023-39220-y
  • Primary Citation of Related Structures:  
    8GTA, 8GTB, 8GTC, 8GTD, 8GTF

  • PubMed 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 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.


  • Organizational Affiliation
    • State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major tail protein
A, B, C, D, E
A, B, C, D, E, F
130Dinoroseobacter phage vB_DshS-R4CMutation(s): 0 
UniProt
Find proteins for A0ACD6BAB4 (Dinoroseobacter phage vB_DshS-R4C)
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Go to UniProtKB:  A0ACD6BAB4
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UniProt GroupA0ACD6BAB4
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Distal tail protein
G, H, I, J, K
G, H, I, J, K, L
214Dinoroseobacter phage vB_DshS-R4CMutation(s): 0 
UniProt
Find proteins for A0ACD6BAB5 (Dinoroseobacter phage vB_DshS-R4C)
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UniProt GroupA0ACD6BAB5
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Megatron protein
M, N, O
1,447Dinoroseobacter phage vB_DshS-R4CMutation(s): 0 
UniProt
Find proteins for A0ACD6BAB7 (Dinoroseobacter phage vB_DshS-R4C)
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UniProt GroupA0ACD6BAB7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Hub protein
P, Q, R
291Dinoroseobacter phage vB_DshS-R4CMutation(s): 0 
UniProt
Find proteins for A0ACD6BAB6 (Dinoroseobacter phage vB_DshS-R4C)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease III
AA [auth a],
S,
T,
U,
V,
W,
X,
Y,
Z
230Dinoroseobacter phage vB_DshS-R4CMutation(s): 0 
UniProt
Find proteins for A0ACD6BAB8 (Dinoroseobacter phage vB_DshS-R4C)
Explore A0ACD6BAB8 
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UniProt GroupA0ACD6BAB8
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection