+
Open data
-
Basic information
Entry | Database: PDB / ID: 6tba | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Virion of native gene transfer agent (GTA) particle | ||||||||||||||||||||||||
![]() |
| ||||||||||||||||||||||||
![]() | ![]() | ||||||||||||||||||||||||
Function / homology | ![]() Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein ...Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Phage conserved hypothetical protein BR0599 / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein / Tail completion protein / Protein of unknown function (DUF3168) / ![]() Similarity search - Domain/homology | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Bardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P. | ||||||||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||||||||
![]() | ![]() Title: Structure and mechanism of DNA delivery of a gene transfer agent. Authors: Pavol Bárdy / Tibor Füzik / Dominik Hrebík / Roman Pantůček / J Thomas Beatty / Pavel Plevka / ![]() ![]() 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 ...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. | ||||||||||||||||||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 9.9 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 10443MC ![]() 6tb9C ![]() 6te8C ![]() 6te9C ![]() 6teaC ![]() 6tebC ![]() 6tehC ![]() 6to8C ![]() 6toaC ![]() 6tsuC ![]() 6tsvC ![]() 6tswC ![]() 6tuiC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
-Protein , 3 types, 187 molecules C5X4Y4Z4A5B5N4R4M4Q4O4P4W4U4T4S4K4J4V4L4H4I4A4D4E4F4G4B4C4CP...
#1: Protein | Mass: 40894.988 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 42846.910 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 14420.007 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Uncharacterized ... , 8 types, 101 molecules E3D3A3C3B3A1E2D2A2C2B2ENDNANCNBNALEMDMAMCMBMEIDIAICIBIAGEHDH...
#2: Protein | Mass: 9104.348 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 32996.828 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 20956.354 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 13871.859 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 12403.123 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | Mass: 31690.734 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | Mass: 138527.359 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | Mass: 22985.713 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
---|
-Non-polymers , 1 types, 3 molecules ![](data/chem/img/SF4.gif)
#12: Chemical | ![]() |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
-
Sample preparation
Component |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | |||||||||||||||||||||||||||||||||||||||||||||||||
Natural host | Organism: Rhodobacter capsulatus | |||||||||||||||||||||||||||||||||||||||||||||||||
Virus shell | Name: HK97-like oblate capsid / Diameter: 945 nm / Triangulation number (T number): 3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.8 / Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 42.75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) |
Image scans | Width: 4096 / Height: 4096 |
-
Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 53432 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27724 / Algorithm: BACK PROJECTION Details: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric ...Details: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric reconstruction (EMD-10568) and tape-measure protein density from C3 reconstruction of tail tube (EMD-10570). Shown resoluton value corresponds to the map with lowest resolution (C3 tail tube). Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |