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- PDB-6teb: Tail-baseplate interface of native GTA particle computed with C6 ... -

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Basic information

Entry
Database: PDB / ID: 6teb
TitleTail-baseplate interface of native GTA particle computed with C6 symmetry
Components
  • Distal tail protein Rcc01695
  • Tail tube protein Rcc01691
KeywordsVIRUS / "distal tail protein" / "tail tube" / "oligosaccharide-binding fold" / "tail tube protein"
Function / homologyProtein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Gene transfer agent, major tail protein / Phage major tail protein TP901-1 / Phage tail tube protein / Phage major tail protein, TP901-1 family / TIGR02217 family protein
Function and homology information
Biological speciesRhodobacter capsulatus DE442 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsBardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P.
Funding support Czech Republic, 7items
OrganizationGrant numberCountry
Ministry of Education (Czech Republic)LQ1601 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Ministry of Education (Czech Republic)LM2011033 Czech Republic
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization3041 Czech Republic
Grant Agency of the Czech Republic18-13064S Czech Republic
CitationJournal: 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
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Tail tube protein Rcc01691
B: Tail tube protein Rcc01691
D: Distal tail protein Rcc01695
C: Distal tail protein Rcc01695


Theoretical massNumber of molelcules
Total (without water)74,8114
Polymers74,8114
Non-polymers00
Water0
1
A: Tail tube protein Rcc01691
B: Tail tube protein Rcc01691
D: Distal tail protein Rcc01695
C: Distal tail protein Rcc01695

A: Tail tube protein Rcc01691
B: Tail tube protein Rcc01691
D: Distal tail protein Rcc01695
C: Distal tail protein Rcc01695

A: Tail tube protein Rcc01691
B: Tail tube protein Rcc01691
D: Distal tail protein Rcc01695
C: Distal tail protein Rcc01695


Theoretical massNumber of molelcules
Total (without water)224,43412
Polymers224,43412
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation2
Buried area8090 Å2
ΔGint-51 kcal/mol
Surface area26520 Å2

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Components

#1: Protein Tail tube protein Rcc01691


Mass: 14420.007 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5ATZ7
#2: Protein Distal tail protein Rcc01695


Mass: 22985.713 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus DE442 (bacteria) / References: UniProt: D5AU01

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Rhodobacter capsulatus DE442 gene transfer agent baseplate-tail interface
Type: COMPLEX
Details: region connecting the tail tube with host-recognition device (baseplate), last disk of tail tube and distal tail protein is shown
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rhodobacter capsulatus DE442 (bacteria)
Buffer solutionpH: 7.8 / Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris1
21 mMNaClSodium chloride1
31 mMMgCl21
41 mMCaCl21
50.01 mg/mlBovine serum albumin1
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: -3000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 42.75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3114
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPU2.1image acquisition
4RELION2.1CTF correction
7Coot0.9model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.16model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 42242
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37230 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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