[English] 日本語
![](img/lk-miru.gif)
- EMDB-10478: Tail of native GTA particle computed with helical refinement, C6 ... -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-10478 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Tail of native GTA particle computed with helical refinement, C6 symmetry | ||||||||||||||||||||||||
![]() | tail of native GTA particle, helical refinement, C6 symmetry | ||||||||||||||||||||||||
![]() |
| ||||||||||||||||||||||||
![]() | "helical refinement" / "tape measure protein" / "bacteriophage" / "tail tube" / VIRUS | ||||||||||||||||||||||||
Function / homology | Gene transfer agent, major tail protein / Phage major tail protein TP901-1 / Phage tail tube protein / Phage major tail protein, TP901-1 family![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.89 Å | ||||||||||||||||||||||||
![]() | Bardy P / Fuzik T | ||||||||||||||||||||||||
Funding support | ![]()
| ||||||||||||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 4.3 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 125.4 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 406.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 406 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6teaMC ![]() 6tb9C ![]() 6tbaC ![]() 6te8C ![]() 6te9C ![]() 6tebC ![]() 6tehC ![]() 6to8C ![]() 6toaC ![]() 6tsuC ![]() 6tsvC ![]() 6tswC ![]() 6tuiC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | tail of native GTA particle, helical refinement, C6 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.063 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : Rhodobacter capsulatus DE442 gene transfer agent tail tube
Entire | Name: Rhodobacter capsulatus DE442 gene transfer agent tail tube |
---|---|
Components |
|
-Supramolecule #1: Rhodobacter capsulatus DE442 gene transfer agent tail tube
Supramolecule | Name: Rhodobacter capsulatus DE442 gene transfer agent tail tube type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: tubular structure interconnecting head to baseplate (host recognition device), partial |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 350 KDa |
-Macromolecule #1: Phage major tail protein, TP901-1 family
Macromolecule | Name: Phage major tail protein, TP901-1 family / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.420007 KDa |
Sequence | String: MAAQNGKDLL IKLDLTGSGQ FETIAGLRAT RISFNAETVD VTSLESQGGW RELLGGAGVR SASISGAGVF KDADTDERAR QIFFDGEVP EFQVIIPDFG IVQGPFMITS IDYAGSHNGE ASYELAMASA GALSFTAI UniProtKB: Phage major tail protein, TP901-1 family |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | helical reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 20 mg/mL | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 |
---|---|
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 / Number grids imaged: 1 / Number real images: 3114 / Average exposure time: 1.0 sec. / 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 / Nominal magnification: 75000 |
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 |
---|---|
Output model | ![]() PDB-6tea: |