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- EMDB-10571: Baseplate of empty GTA particle computed with C3 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-10571
TitleBaseplate of empty GTA particle computed with C3 symmetry
Map data
SampleRhodobacter capsulatus DE442 gene transfer agent baseplate:
(Putative gene transfer agent ...) x 3 / Tail fiber protein Rcc00171
Function / homology
Function and homology information


Protein of unknown function DUF2460 / Bacteriophage phiJL001, Gp84 / Glycoside hydrolase superfamily / Bacteriophage phiJL001, Gp84, C-terminal / Bacteriophage phiJL001, Gp84, N-terminal / GTA TIM-barrel-like domain / Tip attachment protein J
Putative gene transfer agent protein / Putative gene transfer agent protein / Putative gene transfer agent protein
Biological speciesRhodobacter capsulatus DE442 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.49 Å
AuthorsBardy P / Fuzik T / Hrebik D / Pantucek R / Beatty JT / Plevka P
Funding support Czech Republic, 7 items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LQ1601 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Ministry of Education (MoE, Czech Republic)LM2011033 Czech Republic
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization (EMBO)3041 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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 21, 2019-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0557
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0557
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10571.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318.9 Å
1.06 Å/pix.
x 300 pix.
= 318.9 Å
1.06 Å/pix.
x 300 pix.
= 318.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density
Contour LevelBy AUTHOR: 0.0557 / Movie #1: 0.0557
Minimum - Maximum-0.11004337 - 0.39625853
Average (Standard dev.)0.0014252156 (±0.009959277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 318.9 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z318.900318.900318.900
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1100.3960.001

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Supplemental data

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Sample components

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Entire Rhodobacter capsulatus DE442 gene transfer agent baseplate

EntireName: Rhodobacter capsulatus DE442 gene transfer agent baseplate
Details: host recognition device present at the tip of the tail, empty particle
Number of components: 5

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Component #1: protein, Rhodobacter capsulatus DE442 gene transfer agent baseplate

ProteinName: Rhodobacter capsulatus DE442 gene transfer agent baseplate
Details: host recognition device present at the tip of the tail, empty particle
Recombinant expression: No
MassTheoretical: 1000 kDa
SourceSpecies: Rhodobacter capsulatus DE442 (bacteria)

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Component #2: protein, Putative gene transfer agent protein

ProteinName: Putative gene transfer agent protein / Recombinant expression: No

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Component #3: protein, Putative gene transfer agent protein

ProteinName: Putative gene transfer agent protein / Recombinant expression: No

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Component #4: protein, Putative gene transfer agent protein

ProteinName: Putative gene transfer agent protein / Recombinant expression: No

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Component #5: protein, Tail fiber protein Rcc00171

ProteinName: Tail fiber protein Rcc00171 / Recombinant expression: No

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 20 mg/mL
Buffer solution: G-buffer, doi: 10.1016/0003-9861(77)90508-2
pH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 42.75 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1000.0 - -3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3114

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 26978
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 4.49 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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