6TUI

Virion of empty GTA particle


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report



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: 10.1038/s41467-020-16669-9
  • Primary Citation of Related Structures:  
    6TOA, 6TO8, 6TSV, 6TSU, 6TSW, 6TUI, 6TBA, 6TB9, 6TEB, 6TEA

  • 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 un ...

    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

    Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic. pavel.plevka@ceitec.muni.cz.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phage major capsid protein, HK97 familyA4A5B4B5C4C5D4E4F4G4H4I4J4K4L4M4N4O4P4Q4R4S4T4U4V4W4X4Y4Z4385Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01687
Find proteins for D5ATZ3 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Go to UniProtKB:  D5ATZ3
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinA1A2A3B2B3C2C3D2D3E2E384Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01079
Find proteins for D5AR33 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Go to UniProtKB:  D5AR33
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized proteinF2F3325Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01080
Find proteins for D5AR34 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Go to UniProtKB:  D5AR34
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tail tube protein Rcc01691GHIJ137Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01691
Find proteins for D5ATZ7 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Adaptor protein Rcc01688CD197Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01688
Find proteins for D5ATZ4 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Portal protein Rcc01684AB396Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01684
Find proteins for D5ATZ0 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Tail terminator protein Rcc01690F135Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01690
Find proteins for D5ATZ6 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Stopper protein Rcc01689E112Rhodobacter capsulatus SB 1003Mutation(s): 0 
Gene Names: RCAP_rcc01689
Find proteins for D5ATZ5 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
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Go to UniProtKB:  D5ATZ5
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

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

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 

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