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- EMDB-0010: The baseplate complex from the type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-0010
TitleThe baseplate complex from the type VI secretion system
Map data
SampleComplex of TssK, TssF and TssG, components of the type VI secretion system baseplate:
TssG / TssK
Function / homologyType VI secretion system TssK / Type VI secretion, TssG-like / Uncharacterized protein / Type VI secretion system protein ImpH / Uncharacterized protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsRapisarda C / Fronzes R
CitationJournal: Nat Microbiol / Year: 2018
Title: Biogenesis and structure of a type VI secretion baseplate.
Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi ...Authors: Yassine Cherrak / Chiara Rapisarda / Riccardo Pellarin / Guillaume Bouvier / Benjamin Bardiaux / Fabrice Allain / Christian Malosse / Martial Rey / Julia Chamot-Rooke / Eric Cascales / Rémi Fronzes / Eric Durand /
Abstract: To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among ...To support their growth in a competitive environment and cause pathogenesis, bacteria have evolved a broad repertoire of macromolecular machineries to deliver specific effectors and toxins. Among these multiprotein complexes, the type VI secretion system (T6SS) is a contractile nanomachine that targets both prokaryotic and eukaryotic cells. The T6SS comprises two functional subcomplexes: a bacteriophage-related tail structure anchored to the cell envelope by a membrane complex. As in other contractile injection systems, the tail is composed of an inner tube wrapped by a sheath and built on the baseplate. In the T6SS, the baseplate is not only the tail assembly platform, but also docks the tail to the membrane complex and hence serves as an evolutionary adaptor. Here we define the biogenesis pathway and report the cryo-electron microscopy (cryo-EM) structure of the wedge protein complex of the T6SS from enteroaggregative Escherichia coli (EAEC). Using an integrative approach, we unveil the molecular architecture of the whole T6SS baseplate and its interaction with the tail sheath, offering detailed insights into its biogenesis and function. We discuss architectural and mechanistic similarities but also reveal key differences with the T4 phage and Mu phage baseplates.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMay 15, 2018-
Header (metadata) releaseJun 20, 2018-
Map releaseOct 17, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gj3
  • Surface level: 6
  • 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_0010.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 450 pix.
= 495. Å
1.1 Å/pix.
x 450 pix.
= 495. Å
1.1 Å/pix.
x 450 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 6 / Movie #1: 6
Minimum - Maximum-13.500279 - 32.492695
Average (Standard dev.)0.00000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z495.000495.000495.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-13.50032.4930.000

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Supplemental data

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Sample components

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Entire Complex of TssK, TssF and TssG, components of the type VI secreti...

EntireName: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate
Number of components: 3

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Component #1: cellular-component, Complex of TssK, TssF and TssG, components of...

Cellular-componentName: Complex of TssK, TssF and TssG, components of the type VI secretion system baseplate
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: protein, TssG

ProteinName: TssG / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.983488 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #3: protein, TssK

ProteinName: TssK / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 49.999223 kDa
SourceSpecies: Escherichia coli (E. coli)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

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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: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700.0 - 2000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 32504
3D reconstructionSoftware: RELION / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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