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- EMDB-4561: STA of TssJLM -

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Basic information

Entry
Database: EMDB / ID: EMD-4561
TitleSTA of TssJLM
Map dataTssJLM average as obtained by STA
Sample
  • Complex: Membrane complex of the type 6 secretion system
Biological speciesEscherichia coli 042 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 25.0 Å
AuthorsKooger R
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
European Research Council Switzerland
CitationJournal: EMBO J / Year: 2019
Title: and high-resolution cryo-EM structure of a bacterial type VI secretion system membrane complex.
Authors: Chiara Rapisarda / Yassine Cherrak / Romain Kooger / Victoria Schmidt / Riccardo Pellarin / Laureen Logger / Eric Cascales / Martin Pilhofer / Eric Durand / Rémi Fronzes /
Abstract: Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is ...Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to phages. It is composed of a phage tail-like structure inserted in the bacterial cell envelope by a membrane complex (MC) comprising the TssJ, TssL and TssM proteins. We previously reported the low-resolution negative-stain electron microscopy structure of the enteroaggregative MC and proposed a rotational 5-fold symmetry with a TssJ:TssL:TssM stoichiometry of 2:2:2. Here, cryo-electron tomography analyses of the T6SS MC confirm the 5-fold symmetry and identify the regions of the structure that insert into the bacterial membranes. A high-resolution model obtained by single-particle cryo-electron microscopy highlights new features: five additional copies of TssJ, yielding a TssJ:TssL:TssM stoichiometry of 3:2:2, an 11-residue loop in TssM, protruding inside the lumen of the MC and constituting a functionally important periplasmic gate, and hinge regions. Based on these data, we propose an updated model on MC structure and dynamics during T6SS assembly and function.
History
DepositionJan 21, 2019-
Header (metadata) releaseMar 27, 2019-
Map releaseMar 27, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 113
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 113
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4561.png

Downloads & links

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Map

FileDownload / File: emd_4561.map.gz / Format: CCP4 / Size: 501 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTssJLM average as obtained by STA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.9 Å/pix.
x 40 pix.
= 275.92 Å		6.9 Å/pix.
x 80 pix.
= 551.84 Å		6.9 Å/pix.
x 40 pix.
= 275.92 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: 6.898 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 113 / Movie #1: 113
Minimum - Maximum93.403 - 140.06
Average (Standard dev.)110.36105 (±3.5752475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions804040
Spacing408040
CellA: 275.91998 Å / B: 551.83997 Å / C: 275.91998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.8986.8986.898
M x/y/z408040
origin x/y/z0.0000.0000.000
length x/y/z275.920551.840275.920
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS408040
D min/max/mean93.403140.060110.361

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Supplemental data

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Sample components

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Entire : Membrane complex of the type 6 secretion system

EntireName: Membrane complex of the type 6 secretion system
Components
  • Complex: Membrane complex of the type 6 secretion system

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Supramolecule #1: Membrane complex of the type 6 secretion system

SupramoleculeName: Membrane complex of the type 6 secretion system / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli 042 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightExperimental: 1.7 MDa

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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
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 30 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 3.0 sec. / Average electron dose: 1.3 e/Å2
Details: STA from various tomograms taken with slightly different electron dose and frame
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

Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 15000
ExtractionNumber tomograms: 14 / Number images used: 25276 / Reference model: one single particle
Final angle assignmentType: OTHER

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