6TSW

Isometric capsid of empty GTA particle computed with I4(I,n25r) symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure and mechanism of DNA delivery of a gene transfer agent.

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

(2020) Nat Commun 11: 3034-3034

  • DOI: 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Major capsid protein Rcc01687C [auth A],
A [auth B],
B [auth C]
386Rhodobacter capsulatus DE442Mutation(s): 0 
UniProt
Find proteins for D5ATZ3 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5ATZ3 
Go to UniProtKB:  D5ATZ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5ATZ3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.03 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release