+Open data
-Basic information
Entry | Database: PDB / ID: 6teh | ||||||||||||||||||||||||
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Title | Baseplate of native GTA particle computed with C3 symmetry | ||||||||||||||||||||||||
Components | (Putative gene transfer agent protein) x 3 | ||||||||||||||||||||||||
Keywords | VIRUS / "baseplate" / "tail" / "oligosaccharide-binding fold" / "hub" | ||||||||||||||||||||||||
Function / homology | Function and homology information Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Tip attachment protein J ...Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Uncharacterized conserved protein (DUF2163) / GTA TIM-barrel-like domain / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Tip attachment protein J / Putative phage tail protein / Glycoside hydrolase superfamily Similarity search - Domain/homology | ||||||||||||||||||||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.99 Å | ||||||||||||||||||||||||
Authors | Bardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P. | ||||||||||||||||||||||||
Funding support | Czech Republic, 7items
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Citation | Journal: Nat Commun / Year: 2020 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6teh.cif.gz | 199.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6teh.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 6teh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6teh_validation.pdf.gz | 853.8 KB | Display | wwPDB validaton report |
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Full document | 6teh_full_validation.pdf.gz | 870.8 KB | Display | |
Data in XML | 6teh_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 6teh_validation.cif.gz | 59 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/6teh ftp://data.pdbj.org/pub/pdb/validation_reports/te/6teh | HTTPS FTP |
-Related structure data
Related structure data | 10490MC 6tb9C 6tbaC 6te8C 6te9C 6teaC 6tebC 6to8C 6toaC 6tsuC 6tsvC 6tswC 6tuiC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 31690.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: A0A9U0 | ||||
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#2: Protein | Mass: 138527.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: A0A9S9 | ||||
#3: Protein | Mass: 22985.713 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / References: UniProt: A0A9T9 #4: Chemical | ChemComp-SF4 / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Rhodobacter capsulatus DE442 gene transfer agent baseplate Type: COMPLEX Details: host recognition device present at the tip of the tail Entity ID: #1-#3 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight |
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Source (natural) | Organism: Rhodobacter capsulatus DE442 (bacteria) | ||||||||||||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||||||||||||
Natural host | Organism: Rhodobacter capsulatus DE442 | ||||||||||||||||||||||||||||||
Virus shell | Name: GTA virion / Diameter: 870 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 | ||||||||||||||||||||||||||||||
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / 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 |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / 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: 42242 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42242 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |