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- EMDB-20712: In vivo structure of the Legionella type II secretion system by e... -

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Basic information

Entry
Database: EMDB / ID: EMD-20712
TitleIn vivo structure of the Legionella type II secretion system by electron cryotomography (aligning the IM-complex).Type II secretion system
Map dataSubtomogram average of the Legionella pneumophila type II secretion system (aligning the IM-complex).Type II secretion system
Sample
  • Complex: Subtomogram average of the Legionella pneumophila type II secretion system (aligning the IM-complex).Type II secretion system
Biological speciesLegionella pneumophila (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 50.0 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 Gram- ...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 11, 2019-
Current statusDec 11, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.51
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.51
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20712.png

Downloads & links

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Map

FileDownload / File: emd_20712.map.gz / Format: CCP4 / Size: 3.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of the Legionella pneumophila type II secretion system (aligning the IM-complex).
Voxel sizeX=Y=Z: 8.4 Å
Density
Contour LevelBy AUTHOR: 0.39 / Movie #1: 0.51
Minimum - Maximum0 - 1
Average (Standard dev.)0.41985744 (±0.24067993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1268080
Spacing8012680
CellA: 672.0 Å / B: 1058.3999 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/z8012680
origin x/y/z0.0000.0000.000
length x/y/z672.0001058.400672.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS8012680
D min/max/mean0.0001.0000.420

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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 IM-complex).Type II secretion system
Components
  • Complex: Subtomogram average of the Legionella pneumophila type II secretion system (aligning the IM-complex).Type II secretion system

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Supramolecule #1: Subtomogram average of the Legionella pneumophila type II secreti...

SupramoleculeName: Subtomogram average of the Legionella pneumophila type II secretion system (aligning the IM-complex).
type: complex / ID: 1 / Parent: 0
Details: We used electron cryotomography and subtomogram averaging to visualize L. pneumophila type II secretion system complex directly in intact, frozen-hydrated bacterial 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 1993 / Number images used: 440 / Software - Name: PEET
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 50.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMOD / Number subtomograms used: 440

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