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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-10443 | ||||||||||||||||||||||||
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Title | Virion of native gene transfer agent (GTA) particle | ||||||||||||||||||||||||
![]() | virion of native GTA particle | ||||||||||||||||||||||||
![]() | Rhodobacter capsulatus DE442 != Rhodobacter capsulatus SB 1003 Rhodobacter capsulatus DE442
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![]() | "virion" / "horizontal gene transfer" / "gene delivery" / "HK97" / VIRUS | ||||||||||||||||||||||||
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) / Gene transfer agent, major tail protein / Phage portal protein, HK97 / Bacteriophage SPP1, head-tail adaptor / Phage head-tail joining protein / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Tip attachment protein J / Putative phage tail 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 | ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.54 Å | ||||||||||||||||||||||||
![]() | Bardy P / Fuzik T | ||||||||||||||||||||||||
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 | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 76.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 34.7 KB 34.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 9.2 KB 9.2 KB 9.1 KB 10.7 KB 10.7 KB 18.1 KB 18.1 KB | Display Display Display Display Display Display Display | ![]() |
Images | ![]() | 87.5 KB | ||
Filedesc metadata | ![]() | 9.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 228.2 KB | Display | ![]() |
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Full document | ![]() | 227.3 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tbaMC ![]() 6tb9C ![]() 6te8C ![]() 6te9C ![]() 6teaC ![]() 6tebC ![]() 6tehC ![]() 6to8C ![]() 6toaC ![]() 6tsuC ![]() 6tsvC ![]() 6tswC ![]() 6tuiC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | virion of native GTA particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Rhodobacter capsulatus DE442
+Supramolecule #1: Rhodobacter capsulatus SB 1003
+Supramolecule #2: Capsid
+Supramolecule #3: Head spike
+Supramolecule #4: Connector
+Supramolecule #5: Tail
+Supramolecule #6: Baseplate
+Macromolecule #1: Phage major capsid protein, HK97 family
+Macromolecule #2: Uncharacterized protein
+Macromolecule #3: Uncharacterized protein
+Macromolecule #4: Uncharacterized protein
+Macromolecule #5: Portal protein Rcc01684
+Macromolecule #6: Uncharacterized protein
+Macromolecule #7: Uncharacterized protein
+Macromolecule #8: Phage major tail protein, TP901-1 family
+Macromolecule #9: Uncharacterized protein
+Macromolecule #10: Uncharacterized protein
+Macromolecule #11: Uncharacterized protein
+Macromolecule #12: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 20 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.8 Component:
Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2 | ||||||||||||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 42.75 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -3.0 µm / Nominal defocus min: -1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-6tba: |