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- PDB-6tsw: Isometric capsid of empty GTA particle computed with I4(I,n25r) s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tsw | ||||||||||||||||||||||||
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Title | Isometric capsid of empty GTA particle computed with I4(I,n25r) symmetry | ||||||||||||||||||||||||
![]() | Major capsid protein Rcc01687 | ||||||||||||||||||||||||
![]() | VIRUS / "capsid" / "mutant" / "variant" / "HK97" | ||||||||||||||||||||||||
Function / homology | Phage capsid / Phage capsid family / Phage major capsid protein, HK97 family![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.03 Å | ||||||||||||||||||||||||
![]() | Bardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160 KB | Display | ![]() |
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PDB format | ![]() | 125.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10567MC ![]() 6tb9C ![]() 6tbaC ![]() 6te8C ![]() 6te9C ![]() 6teaC ![]() 6tebC ![]() 6tehC ![]() 6to8C ![]() 6toaC ![]() 6tsuC ![]() 6tsvC ![]() 6tuiC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 40982.066 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Rhodobacter capsulatus DE442 gene transfer agent capsid Type: COMPLEX Details: T=3 isometric capsid of GTA particle, population variant. One percent of observed particles contained this assembly. Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||||||||||||
Natural host | Organism: Rhodobacter capsulatus | ||||||||||||||||||||||||||||||
Virus shell | Name: HK97-like capsid / Diameter: 380 nm / Triangulation number (T number): 3 | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.8 / Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -3000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 42.75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3114 |
Image scans | Width: 4096 / Height: 4096 |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1076 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 898 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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