6TUI

Virion of empty GTA particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.0 of the entry. See complete history


Literature

Virion of empty GTA particle

Bardy, P.Fuzik, T.Hrebik, D.Pantucek, R.Beatty, J.T.Plevka, P.

(2020) Nat Commun 11: 3034

  • DOI: https://doi.org/10.1038/s41467-020-16669-9
  • Primary Citation of Related Structures:  
    6TB9, 6TBA, 6TE8, 6TE9, 6TEA, 6TEB, 6TEH, 6TO8, 6TOA, 6TSU, 6TSV, 6TSW, 6TUI

  • PubMed Abstract: 

    Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.


  • Organizational Affiliation

    Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phage major capsid protein, HK97 family385Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ3 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ3
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein84Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5AR33 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5AR33
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinEA [auth F2],
KA [auth F3]
325Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5AR34 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5AR34
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tube protein Rcc01691QA [auth H],
RA [auth I],
SA [auth J],
ZA [auth G]
137Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ7 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Adaptor protein Rcc01688TA [auth C],
WA [auth D]
197Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ4 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Portal protein Rcc01684UA [auth A],
VA [auth B]
396Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ0 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Tail terminator protein Rcc01690XA [auth F]135Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ6 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Stopper protein Rcc01689YA [auth E]112Rhodobacter capsulatus SB 1003Mutation(s): 0 
UniProt
Find proteins for D5ATZ5 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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UniProt GroupD5ATZ5
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.16
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Czech Republic)Czech RepublicLQ1601
European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0070
Ministry of Education (MoE, Czech Republic)Czech RepublicLM2011033
Czech Science FoundationCzech Republic15-21631Y
Czech Science FoundationCzech Republic18-17810S
European Molecular Biology Organization (EMBO)Czech Republic3041
Grant Agency of the Czech RepublicCzech Republic18-13064S

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release