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- EMDB-9342: Structure of the type VI secretion system TssK-TssF-TssG baseplat... -

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Basic information

Entry
Database: EMDB / ID: EMD-9342
TitleStructure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy - TssK focused map
Map dataTssK focused map
Sample
  • Complex: TssK-TssF-TssG T6SS baseplate subcomplex
Biological speciesEscherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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: 0.075
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.075
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9342.png

Downloads & links

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Map

FileDownload / File: emd_9342.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTssK focused map
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075 / Movie #1: 0.075
Minimum - Maximum-0.20910932 - 0.3792051
Average (Standard dev.)0.00020507124 (±0.0058576344)
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-0.2090.3790.000

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Supplemental data

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Additional map: TssK focused map - unsharpened

Fileemd_9342_additional.map
AnnotationTssK focused map - unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TssK-TssF-TssG T6SS baseplate subcomplex

EntireName: TssK-TssF-TssG T6SS baseplate subcomplex
Components
  • Complex: TssK-TssF-TssG T6SS baseplate subcomplex

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Supramolecule #1: TssK-TssF-TssG T6SS baseplate subcomplex

SupramoleculeName: TssK-TssF-TssG T6SS baseplate subcomplex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli O44:H18 (strain 042 / EAEC) (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.12 mg/mL
BufferpH: 7.8
GridSupport film - Material: CARBON / Support film - topology: CONTINUOUS / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER
Details: An initial model was obtained using cryosparc abinitio.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36496
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)

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