+Open data
-Basic information
Entry | Database: PDB / ID: 6tba | ||||||||||||||||||||||||
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Title | Virion of native gene transfer agent (GTA) particle | ||||||||||||||||||||||||
Components |
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Keywords | VIRUS / "virion" / "horizontal gene transfer" / "gene delivery" / "HK97" | ||||||||||||||||||||||||
Function / homology | Function and homology information 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) / Gene transfer agent, major tail protein / Phage portal protein, HK97 / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Tip attachment protein J / Putative phage tail protein / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage major tail protein TP901-1 / Phage tail tube protein / Phage capsid / Phage capsid family / Glycoside hydrolase superfamily Similarity search - Domain/homology | ||||||||||||||||||||||||
Biological species | Rhodobacter capsulatus SB 1003 (bacteria) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.54 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 | 6tba.cif.gz | 9.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6tba.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6tba.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tba ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tba | HTTPS FTP |
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-Related structure data
Related structure data | 10443MC 6tb9C 6te8C 6te9C 6teaC 6tebC 6tehC 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
-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) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ3 #5: Protein | Mass: 42846.910 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ0 #8: Protein | Mass: 14420.007 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ7 |
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-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) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AR33 #3: Protein | Mass: 32996.828 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AR34 #4: Protein | Mass: 20956.354 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ4 #6: Protein | Mass: 13871.859 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ6 #7: Protein | Mass: 12403.123 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ5 #9: Protein | Mass: 31690.734 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AU02 #10: Protein | Mass: 138527.359 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AU04 #11: Protein | Mass: 22985.713 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AU01 |
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-Non-polymers , 1 types, 3 molecules
#12: Chemical |
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-Details
Has ligand of interest | N |
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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 |
-Sample preparation
Component |
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Molecular weight |
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Source (natural) |
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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 |
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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 FIELDBright-field microscopy / 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 | 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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 53432 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
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 |