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- EMDB-20713: In vivo structure of the Legionella type II secretion system by e... -

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Basic information

Entry
Database: EMDB / ID: EMD-20713
TitleIn vivo structure of the Legionella type II secretion system by electron cryotomography (aligning the OM-complex).Type II secretion system
Map dataType II secretion system
SampleSubtomogram average of the Legionella pneumophila type II secretion system (aligning the OM-complex).Type II secretion system
Biological speciesLegionella pneumophila (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 40 Å
AuthorsGhosal D / Jensen GJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01AI127401 United States
CitationJournal: Nat Microbiol / Year: 2019
Title: In vivo structure of the Legionella type II secretion system by electron cryotomography.
Authors: Debnath Ghosal / Ki Woo Kim / Huaixin Zheng / Mohammed Kaplan / Hilary K Truchan / Alberto E Lopez / Ian E McIntire / Joseph P Vogel / Nicholas P Cianciotto / Grant J Jensen /
Abstract: The type II secretion system (T2SS) is a multiprotein envelope-spanning assembly that translocates a wide range of virulence factors, enzymes and effectors through the outer membrane of many ...The type II secretion system (T2SS) is a multiprotein envelope-spanning assembly that translocates a wide range of virulence factors, enzymes and effectors through the outer membrane of many Gram-negative bacteria. Here, using electron cryotomography and subtomogram averaging methods, we reveal the in vivo structure of an intact T2SS imaged within the human pathogen Legionella pneumophila. Although the T2SS has only limited sequence and component homology with the evolutionarily related type IV pilus (T4P) system, we show that their overall architectures are remarkably similar. Despite similarities, there are also differences, including, for example, that the T2SS-ATPase complex is usually present but disengaged from the inner membrane, the T2SS has a much longer periplasmic vestibule and it has a short-lived flexible pseudopilus. Placing atomic models of the components into our electron cryotomography map produced a complete architectural model of the intact T2SS that provides insights into the structure and function of its components, its position within the cell envelope and the interactions between its different subcomplexes.
History
DepositionSep 12, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseDec 4, 2019-
UpdateDec 4, 2019-
Current statusDec 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.42
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.42
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20713.map.gz / Format: CCP4 / Size: 2.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.4 Å/pix.
x 80 pix.
= 672. Å
8.4 Å/pix.
x 120 pix.
= 1008. Å
8.4 Å/pix.
x 80 pix.
= 672. 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
Contour LevelBy AUTHOR: 0.42 / Movie #1: 0.42
Minimum - Maximum0 - 1
Average (Standard dev.)0.31244212 (±0.2016792)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1208080
Spacing8012080
CellA: 672.0 Å / B: 1007.99994 Å / C: 672.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.48.48.4
M x/y/z8012080
origin x/y/z0.0000.0000.000
length x/y/z672.0001008.000672.000
α/β/γ90.00090.00090.000
start NX/NY/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS8012080
D min/max/mean0.0001.0000.312

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Supplemental data

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Sample components

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Entire Subtomogram average of the Legionella pneumophila type II secreti...

EntireName: Subtomogram average of the Legionella pneumophila type II secretion system (aligning the OM-complex).Type II secretion system
Details: We used electron cryotomography and subtomogram averaging to visualize L. pneumophila type II secretion system complex directly in intact, frozen-hydrated bacterial cells
Number of components: 1

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Component #1: protein, Subtomogram average of the Legionella pneumophila type I...

ProteinName: Subtomogram average of the Legionella pneumophila type II secretion system (aligning the OM-complex).Type II secretion system
Details: We used electron cryotomography and subtomogram averaging to visualize L. pneumophila type II secretion system complex directly in intact, frozen-hydrated bacterial cellsType II secretion system
Recombinant expression: No
SourceSpecies: Legionella pneumophila (bacteria) / Strain: Lp02

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Experimental details

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Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 6.9
VitrificationCryogen name: OTHER

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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: 1.2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C2 (2 fold cyclic) / Number of subtomograms: 440
3D reconstructionSoftware: IMOD / Resolution: 40 Å / Resolution method: FSC 0.143 CUT-OFF

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