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- EMDB-9343: Structure of the type VI secretion system TssK-TssF-TssG baseplat... -

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Basic information

Entry
Database: EMDB / ID: EMD-9343
TitleStructure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy - TssK focused mapType VI secretion system
Map dataType VI secretion system
SampleTssK-TssF-TssG T6SS baseplate subcomplex
Biological speciesEscherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPark YJ / Lacourse KD / Cambillau C / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / DiMaio F / Mougous JD / Veesler D
CitationJournal: Nat Commun / Year: 2018
Title: Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy.
Authors: Young-Jun Park / Kaitlyn D Lacourse / Christian Cambillau / Frank DiMaio / Joseph D Mougous / David Veesler /
Abstract: Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although ...Type VI secretion systems (T6SSs) translocate effectors into target cells and are made of a contractile sheath and a tube docked onto a multi-protein transmembrane complex via a baseplate. Although some information is available about the mechanisms of tail contraction leading to effector delivery, the detailed architecture and function of the baseplate remain unknown. Here, we report the 3.7 Å resolution cryo-electron microscopy reconstruction of an enteroaggregative Escherichia coli baseplate subcomplex assembled from TssK, TssF and TssG. The structure reveals two TssK trimers interact with a locally pseudo-3-fold symmetrical complex comprising two copies of TssF and one copy of TssG. TssF and TssG are structurally related to each other and to components of the phage T4 baseplate and of the type IV secretion system, strengthening the evolutionary relationships among these macromolecular machines. These results, together with bacterial two-hybrid assays, provide a structural framework to understand the T6SS baseplate architecture.
History
DepositionNov 14, 2018-
Header (metadata) releaseDec 12, 2018-
Map releaseDec 26, 2018-
UpdateJan 9, 2019-
Current statusJan 9, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9343.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 288 pix.
= 394.56 Å
1.37 Å/pix.
x 288 pix.
= 394.56 Å
1.37 Å/pix.
x 288 pix.
= 394.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.15136221 - 0.30378425
Average (Standard dev.)0.00018014754 (±0.0044516306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 394.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z394.560394.560394.560
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1510.3040.000

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Supplemental data

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Additional map: TssF-TssG focused map - unsharpened

Fileemd_9343_additional.map
AnnotationTssF-TssG focused map - unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire TssK-TssF-TssG T6SS baseplate subcomplex

EntireName: TssK-TssF-TssG T6SS baseplate subcomplex / Number of components: 1

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Component #1: protein, TssK-TssF-TssG T6SS baseplate subcomplex

ProteinName: TssK-TssF-TssG T6SS baseplate subcomplex / Recombinant expression: No
SourceSpecies: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.12 mg/mL / pH: 7.8
Support filmunspecified
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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 57567
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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