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- EMDB-8566: In vivo structure of the Legionella pneumophila Dot/Icm type IV s... -

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Entry
Database: EMDB / ID: EMD-8566
TitleIn vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system (aligning the outer membrane complex)
Map dataIn vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system (aligning the outer membrane complex)
Sample
  • Complex: Legionella pneumophila Dot/Icm type IVB secretion system
Biological speciesLegionella pneumophila (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsGhosal D / Chang YW / Jensen GJ
CitationJournal: EMBO Rep / Year: 2017
Title: structure of the Dot/Icm type IV secretion system by electron cryotomography.
Authors: Debnath Ghosal / Yi-Wei Chang / Kwangcheol C Jeong / Joseph P Vogel / Grant J Jensen /
Abstract: Type IV secretion systems (T4SSs) are large macromolecular machines that translocate protein and DNA and are involved in the pathogenesis of multiple human diseases. Here, using electron ...Type IV secretion systems (T4SSs) are large macromolecular machines that translocate protein and DNA and are involved in the pathogenesis of multiple human diseases. Here, using electron cryotomography (ECT), we report the structure of the Dot/Icm type IVB secretion system (T4BSS) utilized by the human pathogen This is the first structure of a type IVB secretion system, and also the first structure of any T4SS While the Dot/Icm system shares almost no sequence similarity with type IVA secretion systems (T4ASSs), its overall structure is seen here to be remarkably similar to previously reported T4ASS structures (those encoded by the R388 plasmid in and the cag pathogenicity island in ). This structural similarity suggests shared aspects of mechanism. However, compared to the negative-stain reconstruction of the purified T4ASS from the R388 plasmid, the Dot/Icm system is approximately twice as long and wide and exhibits several additional large densities, reflecting type-specific elaborations and potentially better structural preservation .
History
DepositionJan 20, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseMar 29, 2017-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8566.png

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Map

FileDownload / File: emd_8566.map.gz / Format: CCP4 / Size: 4.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system (aligning the outer membrane complex)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.4 Å/pix.
x 100 pix.
= 840. Å		8.4 Å/pix.
x 120 pix.
= 1008. Å		8.4 Å/pix.
x 100 pix.
= 840. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum0. - 1.
Average (Standard dev.)0.40672174 (±0.19024341)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions120100100
Spacing100120100
CellA: 839.99994 Å / B: 1007.99994 Å / C: 839.99994 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.48.48.4
M x/y/z100120100
origin x/y/z0.0000.0000.000
length x/y/z840.0001008.000840.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100120100
D min/max/mean0.0001.0000.407

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Supplemental data

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Sample components

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Entire : Legionella pneumophila Dot/Icm type IVB secretion system

EntireName: Legionella pneumophila Dot/Icm type IVB secretion system
Components
  • Complex: Legionella pneumophila Dot/Icm type IVB secretion system

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Supramolecule #1: Legionella pneumophila Dot/Icm type IVB secretion system

SupramoleculeName: Legionella pneumophila Dot/Icm type IVB secretion system
type: complex / ID: 1 / Parent: 0
Details: We used electron cryotomography and subtomogram averaging to visualize L. pneumophila Dot/Icm machines directly in intact, frozen-hydrated bacteria cells.
Source (natural)Organism: Legionella pneumophila (bacteria) / Strain: Lp02

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6.9
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: IMOD, TOMO3D / Details: RESMAP / Number subtomograms used: 373
ExtractionNumber tomograms: 87 / Number images used: 386 / Software - Name: PEET
Final angle assignmentType: OTHER

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