8GTD | pdb_00008gtd

Cryo-EM model of the marine siphophage vB_DshS-R4C portal-adaptor complex

• PDB DOI: https://doi.org/10.2210/pdb8GTD/pdb
• EM Map EMD-34250: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Dinoroseobacter phage vB_DshS-R4C
• Mutation(s): No 


• Deposited: 2022-09-08 Released: 2023-07-12 
• Deposition Author(s): Huang, Y., Sun, H., Wei, S., Zheng, Q., Li, S., Zhang, R., Xia, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 37330604 
• DOI: https://doi.org/10.1038/s41467-023-39220-y
• Primary Citation 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.

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Organizational Affiliation: 
• State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China.
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China.
State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China.
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China. [e-mail].
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China. [e-mail].
State Key Laboratory of Marine Environmental Science, Fujian Key Laboratory of Marine Carbon Sequestration, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China. [e-mail].
Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China. [e-mail].
State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, School of Life Sciences, Xiamen University, Xiamen, 361102, China. [e-mail].
National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, 361102, China. [e-mail].
Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen, 361102, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C12  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 955.24 kDa 
• Atom Count: 29,580 
• Modeled Residue Count: 7,392 
• Deposited Residue Count: 8,748 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Portal protein	A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H], Q [auth I], S [auth J], U [auth K], W [auth L]	551	Dinoroseobacter phage vB_DshS-R4C	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAB1 (Dinoroseobacter phage vB_DshS-R4C) Explore A0ACD6BAB1  Go to UniProtKB:  A0ACD6BAB1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Head-to-tail joining protein	B [auth M], D [auth N], F [auth O], H [auth P], J [auth Q], L [auth R], N [auth S], P [auth T], R [auth U], T [auth V], V [auth W], X	178	Dinoroseobacter phage vB_DshS-R4C	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAB0 (Dinoroseobacter phage vB_DshS-R4C) Explore A0ACD6BAB0  Go to UniProtKB:  A0ACD6BAB0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Huang, Y., Sun, H., Wei, S., Zheng, Q., Li, S., Zhang, R., Xia, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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