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- EMDB-8569: In vivo structure of the Legionella pneumophila Dot/Icm type IV s... -

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Basic information

Entry
Database: EMDB / ID: EMD-8569
TitleIn vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system core complex (aligning the inner membrane part)Secretion
Map dataCommunication In vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system core complex (aligning the inner membrane part)
Sample
  • Complex: Legionella pneumophila Dot/Icm type IVB secretion system core complex (inner membrane complex)
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: 0.667
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.667
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_8569.map.gz / Format: CCP4 / Size: 4.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCommunication In vivo structure of the Legionella pneumophila Dot/Icm type IV secretion system core complex (aligning the inner membrane part)
Voxel sizeX=Y=Z: 8.4 Å
Density
Contour LevelBy AUTHOR: 0.667 / Movie #1: 0.667
Minimum - Maximum-0.00000011920929 - 1.
Average (Standard dev.)0.46630684 (±0.18731318)
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/mean-0.0001.0000.466

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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 core com...

EntireName: Legionella pneumophila Dot/Icm type IVB secretion system core complex (inner membrane complex)
Components
  • Complex: Legionella pneumophila Dot/Icm type IVB secretion system core complex (inner membrane complex)

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

SupramoleculeName: Legionella pneumophila Dot/Icm type IVB secretion system core complex (inner membrane complex)
type: complex / ID: 1 / Parent: 0
Details: We used electron cryotomography and subtomogram averaging to visualize L. pneumophila Dot/Icm core complex 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
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: 73 / Number images used: 261 / Software - Name: PEET
Final angle assignmentType: OTHER
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: 261

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