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- EMDB-3878: The distal end of a non-contractile T6SS sheath. -

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Basic information

Entry
Database: EMDB / ID: EMD-3878
TitleThe distal end of a non-contractile T6SS sheath.
Map dataThe distal end of a non-contractile T6SS sheath.
Sample
  • Organelle or cellular component: The distal end of a non-contractile T6SS sheath.
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsNazarov S / Basler M
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_159525 Switzerland
CitationJournal: EMBO J / Year: 2018
Title: Cryo-EM reconstruction of Type VI secretion system baseplate and sheath distal end.
Authors: Sergey Nazarov / Johannes P Schneider / Maximilian Brackmann / Kenneth N Goldie / Henning Stahlberg / Marek Basler /
Abstract: The bacterial Type VI secretion system (T6SS) assembles from three major parts: a membrane complex that spans inner and outer membranes, a baseplate, and a sheath-tube polymer. The baseplate ...The bacterial Type VI secretion system (T6SS) assembles from three major parts: a membrane complex that spans inner and outer membranes, a baseplate, and a sheath-tube polymer. The baseplate assembles around a tip complex with associated effectors and connects to the membrane complex by TssK. The baseplate assembly initiates sheath-tube polymerization, which in some organisms requires TssA. Here, we analyzed both ends of isolated non-contractile sheaths by cryo-electron microscopy. Our analysis suggests that the baseplate, solved to an average 8.0 Å resolution, is composed of six subunits of TssE/F/G and the baseplate periphery is decorated by six TssK trimers. The VgrG/PAAR tip complex in the center of the baseplate is surrounded by a cavity, which may accommodate up to ~450 kDa of effector proteins. The distal end of the sheath, resolved to an average 7.5 Å resolution, shows sixfold symmetry; however, its protein composition is unclear. Our structures provide an important step toward an atomic model of the complete T6SS assembly.
History
DepositionSep 18, 2017-
Header (metadata) releaseNov 29, 2017-
Map releaseNov 29, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3878.png

Downloads & links

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Map

FileDownload / File: emd_3878.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe distal end of a non-contractile T6SS sheath.
Voxel sizeX=Y=Z: 2.12 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.031882275 - 0.07046513
Average (Standard dev.)0.00021565548 (±0.005372672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.122.122.12
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z542.720542.720542.720
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-0.0320.0700.000

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Supplemental data

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Mask #1

Fileemd_3878_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Histogram (log scale)

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Additional map: The distal end of a non-contractile T6SS sheath. Post-processed map.

Fileemd_3878_additional.map
AnnotationThe distal end of a non-contractile T6SS sheath. Post-processed map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The distal end of a non-contractile T6SS sheath. Post-processed map.

Fileemd_3878_additional_1.map
AnnotationThe distal end of a non-contractile T6SS sheath. Post-processed map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_3878_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_3878_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The distal end of a non-contractile T6SS sheath.

EntireName: The distal end of a non-contractile T6SS sheath.
Components
  • Organelle or cellular component: The distal end of a non-contractile T6SS sheath.

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Supramolecule #1: The distal end of a non-contractile T6SS sheath.

SupramoleculeName: The distal end of a non-contractile T6SS sheath. / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Vibrio cholerae (bacteria) / Strain: 2740-80 / Organelle: T6SS
Molecular weightExperimental: 540 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8.3
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Name: GIF Quantum LS
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 9202 / Average exposure time: 16.0 sec. / Average electron dose: 5.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 21446
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4) / Details: Probability-weighted angular assignment
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1) / Details: Probability-weighted angular assignment
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 3710
FSC plot (resolution estimation)

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