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- EMDB-2567: Structure of a bacterial Type IV secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-2567
TitleStructure of a bacterial Type IV secretion system
Map dataStructure of a bacterial Type IV secretion system
Sample
  • Sample: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmid
  • Protein or peptide: Type IV secretion system from R388 conjugative plasmid
KeywordsType IV secretion system / R388 conjugative plasmid / Escherichia coli / negative stain electron microscopy
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsLow HH / Gubellini F / Rivera-Calzada A / Braun N / Connery S / Dujeancourt A / Lu F / Redzej A / Fronzes R / Orlova EV / Waksman G
CitationJournal: Nature / Year: 2014
Title: Structure of a type IV secretion system.
Authors: Harry H Low / Francesca Gubellini / Angel Rivera-Calzada / Nathalie Braun / Sarah Connery / Annick Dujeancourt / Fang Lu / Adam Redzej / Rémi Fronzes / Elena V Orlova / Gabriel Waksman /
Abstract: Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification ...Bacterial type IV secretion systems translocate virulence factors into eukaryotic cells, distribute genetic material between bacteria and have shown potential as a tool for the genetic modification of human cells. Given the complex choreography of the substrate through the secretion apparatus, the molecular mechanism of the type IV secretion system has proved difficult to dissect in the absence of structural data for the entire machinery. Here we use electron microscopy to reconstruct the type IV secretion system encoded by the Escherichia coli R388 conjugative plasmid. We show that eight proteins assemble in an intricate stoichiometric relationship to form an approximately 3 megadalton nanomachine that spans the entire cell envelope. The structure comprises an outer membrane-associated core complex connected by a central stalk to a substantial inner membrane complex that is dominated by a battery of 12 VirB4 ATPase subunits organized as side-by-side hexameric barrels. Our results show a secretion system with markedly different architecture, and consequently mechanism, to other known bacterial secretion systems.
History
DepositionJan 21, 2014-
Header (metadata) releaseFeb 19, 2014-
Map releaseApr 9, 2014-
UpdateApr 23, 2014-
Current statusApr 23, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 43.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 43.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2567.tif

Downloads & links

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Map

FileDownload / File: emd_2567.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a bacterial Type IV secretion system
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.3 Å/pix.
x 192 pix.
= 633.6 Å		3.3 Å/pix.
x 192 pix.
= 633.6 Å		3.3 Å/pix.
x 192 pix.
= 633.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 43.5 / Movie #1: 43.5
Minimum - Maximum-1000.0 - 2669.0463867200001
Average (Standard dev.)4.89805698 (±67.904029850000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 633.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.33.33.3
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z633.600633.600633.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-207-207-206
NX/NY/NZ414414414
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-1000.0002669.0464.898

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Supplemental data

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Sample components

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Entire : Structure of a bacterial Type IV secretion system from Escherichi...

EntireName: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmid
Components
  • Sample: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmid
  • Protein or peptide: Type IV secretion system from R388 conjugative plasmid

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Supramolecule #1000: Structure of a bacterial Type IV secretion system from Escherichi...

SupramoleculeName: Structure of a bacterial Type IV secretion system from Escherichia coli R388 conjugative plasmid
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 3 MDa / Theoretical: 3.4 MDa
Method: Calculation based on stoichiometry determination of individual components within the complex

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Macromolecule #1: Type IV secretion system from R388 conjugative plasmid

MacromoleculeName: Type IV secretion system from R388 conjugative plasmid
type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: R388 conjugative plasmid
Molecular weightExperimental: 3 MDa / Theoretical: 3.4 MDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant plasmid: pAsk3c

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 8
Details: 50 mM Tris-HCl pH 8.0, 200 mM NaCl, 0.06 % w/v DM-NPG, 0.1 % w/v digitonin, 1 mM DTT and 1mM EDTA
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds.
GridDetails: Glow-discharged carbon-coated copper grids (Agar Scientific)
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJun 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 693 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 45500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 45500
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: OTHER / Number images used: 3200
Final two d classificationNumber classes: 803

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