+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10443 | ||||||||||||||||||||||||
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Title | Virion of native gene transfer agent (GTA) particle | ||||||||||||||||||||||||
Map data | virion of native GTA particle | ||||||||||||||||||||||||
Sample | Rhodobacter capsulatus DE442 != Rhodobacter capsulatus SB 1003 Rhodobacter capsulatus DE442
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Keywords | "virion" / "horizontal gene transfer" / "gene delivery" / "HK97" / VIRUS | ||||||||||||||||||||||||
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) / Phage conserved hypothetical protein / Tail completion protein / Protein of unknown function (DUF3168) / : ...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) / 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 phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / Phage conserved hypothetical protein BR0599 / Phage major tail protein TP901-1 / Tip attachment protein J / Phage tail tube protein / Putative phage tail protein / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / Phage capsid / Phage capsid family / Glycoside hydrolase superfamily Similarity search - Domain/homology | ||||||||||||||||||||||||
Biological species | Rhodobacter capsulatus SB 1003 (bacteria) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.54 Å | ||||||||||||||||||||||||
Authors | Bardy P / Fuzik T | ||||||||||||||||||||||||
Funding support | Czech Republic, 7 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10443.map.gz | 76.7 MB | EMDB map data format | |
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Header (meta data) | emd-10443-v30.xml emd-10443.xml | 34.7 KB 34.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10443_fsc.xml emd_10443_fsc_1.xml emd_10443_fsc_2.xml emd_10443_fsc_3.xml emd_10443_fsc_4.xml emd_10443_fsc_5.xml emd_10443_fsc_6.xml | 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 | FSC data file |
Images | emd_10443.png | 87.5 KB | ||
Filedesc metadata | emd-10443.cif.gz | 9.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10443 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10443 | HTTPS FTP |
-Validation report
Summary document | emd_10443_validation.pdf.gz | 228.2 KB | Display | EMDB validaton report |
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Full document | emd_10443_full_validation.pdf.gz | 227.3 KB | Display | |
Data in XML | emd_10443_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_10443_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10443 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10443 | 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 (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10443.map.gz / Format: CCP4 / Size: 3.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | virion of native GTA particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: FIELD EMISSION GUN |
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 |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-6tba: |