Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structure and mechanism of DNA delivery of a gene transfer agent.
Journal, issue, pages	Nat Commun, Vol. 11, Issue 1, Page 3034, Year 2020
Publish date	Jun 15, 2020
Authors	Pavol Bárdy / Tibor Füzik / Dominik Hrebík / Roman Pantůček / J Thomas Beatty / Pavel Plevka /
PubMed 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.
External links	Nat Commun / PubMed:32541663 / PubMed Central
Methods	EM (single particle) / EM (helical sym.)
Resolution	3.32 - 10.47 Å
Structure data	10442 6tb9 EMDB-10442, PDB-6tb9: Capsid of native GTA particle computed with C5 symmetry Method: EM (single particle) / Resolution: 3.56 Å 10443 6tba EMDB-10443, PDB-6tba: Virion of native gene transfer agent (GTA) particle Method: EM (single particle) / Resolution: 4.54 Å 10476 6te8 EMDB-10476, PDB-6te8: Neck of native GTA particle computed with C12 symmetry Method: EM (single particle) / Resolution: 3.32 Å 10477 6te9 EMDB-10477, PDB-6te9: Neck of native GTA particle computed with C6 symmetry Method: EM (single particle) / Resolution: 3.58 Å 10478 6tea EMDB-10478, PDB-6tea: Tail of native GTA particle computed with helical refinement, C6 symmetry Method: EM (helical sym.) / Resolution: 3.89 Å 10479 6teb EMDB-10479, PDB-6teb: Tail-baseplate interface of native GTA particle computed with C6 symmetry Method: EM (single particle) / Resolution: 4.14 Å 10490 6teh EMDB-10490, PDB-6teh: Baseplate of native GTA particle computed with C3 symmetry Method: EM (single particle) / Resolution: 3.99 Å 10541 6to8 EMDB-10541, PDB-6to8: Neck of empty GTA particle computed with C12 symmetry Method: EM (single particle) / Resolution: 3.36 Å 10542 6toa EMDB-10542, PDB-6toa: Neck of empty GTA particle computed with C6 symmetry Method: EM (single particle) / Resolution: 3.47 Å 10565 6tsu EMDB-10565, PDB-6tsu: Capsid of empty GTA particle computed with C5 symmetry Method: EM (single particle) / Resolution: 3.42 Å 10566 6tsv EMDB-10566, PDB-6tsv: Tail of empty GTA particle computed with helical refinement, C6 symmetry Method: EM (helical sym.) / Resolution: 3.78 Å 10567 6tsw EMDB-10567, PDB-6tsw: Isometric capsid of empty GTA particle computed with I4(I,n25r) symmetry Method: EM (single particle) / Resolution: 4.03 Å EMDB-10568: Capsid-neck interface of native GTA particle, asymmetric reconstruction Method: EM (single particle) / Resolution: 4.25 Å EMDB-10569: Capsid-neck interface of empty GTA particle, asymmetric reconstruction Method: EM (single particle) / Resolution: 4.15 Å EMDB-10570: Tail tube of native GTA particle computed with C3 symmetry Method: EM (single particle) / Resolution: 4.54 Å EMDB-10571: Baseplate of empty GTA particle computed with C3 symmetry Method: EM (single particle) / Resolution: 4.49 Å EMDB-10572: Baseplate of native GTA particle, asymmetric reconstruction Method: EM (single particle) / Resolution: 4.56 Å 10592 6tui EMDB-10592, PDB-6tui: Virion of empty GTA particle Method: EM (single particle) / Resolution: 10.47 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER / Iron–sulfur cluster
Source	rhodobacter capsulatus (bacteria) rhodobacter capsulatus sb 1003 (bacteria) rhodobacter capsulatus de442 (bacteria)
Keywords	VIRUS / "capsid" / "gene transfer agent" / "bacteriophage" / "HK97" / "virion" / "horizontal gene transfer" / "gene delivery" / "portal" / "adaptor" / "neck" / "tail tube" / "helical refinement" / "tape measure protein" / "distal tail protein" / "oligosaccharide-binding fold" / "tail tube protein" / "baseplate" / "tail" / "hub" / "connector" / "jelly roll" / "spike" / "mutant" / "variant" / "genome release"