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- EMDB-7612: Cytoplasmic ATPase in a Type IV Secretion Machine -

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Basic information

Entry
Database: EMDB / ID: EMD-7612
TitleCytoplasmic ATPase in a Type IV Secretion Machine
Map dataCytoplasmic ATPase complex
Sample
  • Complex: Type IV secretion machine
Biological speciesLegionella pneumophila (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsLiu J / Hu B
CitationJournal: Nat Microbiol / Year: 2018
Title: A unique cytoplasmic ATPase complex defines the Legionella pneumophila type IV secretion channel.
Authors: David Chetrit / Bo Hu / Peter J Christie / Craig R Roy / Jun Liu /
Abstract: Type IV secretion systems (T4SSs) are complex machines used by bacteria to deliver protein and DNA complexes into target host cells. Conserved ATPases are essential for T4SS function, but how they ...Type IV secretion systems (T4SSs) are complex machines used by bacteria to deliver protein and DNA complexes into target host cells. Conserved ATPases are essential for T4SS function, but how they coordinate their activities to promote substrate transfer remains poorly understood. Here, we show that the DotB ATPase associates with the Dot-Icm T4SS at the Legionella cell pole through interactions with the DotO ATPase. The structure of the Dot-Icm apparatus was solved in situ by cryo-electron tomography at 3.5 nm resolution and the cytoplasmic complex was solved at 3.0 nm resolution. These structures revealed a cell envelope-spanning channel that connects to the cytoplasmic complex. Further analysis revealed a hexameric assembly of DotO dimers associated with the inner membrane complex, and a DotB hexamer associated with the base of this cytoplasmic complex. The assembly of a DotB-DotO energy complex creates a cytoplasmic channel that directs the translocation of substrates through the T4SS. These data define distinct stages in Dot-Icm machine biogenesis, advance our understanding of channel activation, and identify an envelope-spanning T4SS channel.
History
DepositionMar 23, 2018-
Header (metadata) releaseApr 25, 2018-
Map releaseJun 6, 2018-
UpdateJun 6, 2018-
Current statusJun 6, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7612.png

Downloads & links

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Map

FileDownload / File: emd_7612.map.gz / Format: CCP4 / Size: 1.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCytoplasmic ATPase complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5 Å/pix.
x 60 pix.
= 300. Å		5 Å/pix.
x 80 pix.
= 400. Å		5 Å/pix.
x 80 pix.
= 400. 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: 5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.06
Minimum - Maximum-0.5063938 - 0.47236666
Average (Standard dev.)0.0003300983 (±0.08669998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-30
Dimensions808060
Spacing808060
CellA: 400.0 Å / B: 400.0 Å / C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z555
M x/y/z808060
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000300.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-40-40-30
NC/NR/NS808060
D min/max/mean-0.5060.4720.000

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Supplemental data

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Sample components

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Entire : Type IV secretion machine

EntireName: Type IV secretion machine
Components
  • Complex: Type IV secretion machine

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Supramolecule #1: Type IV secretion machine

SupramoleculeName: Type IV secretion machine / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Legionella pneumophila (bacteria)

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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: 7
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.0 sec. / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 5000
ExtractionNumber tomograms: 1000 / Number images used: 5000 / Method: manually
CTF correctionSoftware - Name: IMOD (ver. 4.9.6)
Final angle assignmentType: OTHER

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