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- EMDB-2524: Cryo EM structure of the contractile Type Six Secretion System Vi... -

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Basic information

Entry
Database: EMDB / ID: EMD-2524
TitleCryo EM structure of the contractile Type Six Secretion System VipA/B complex
Map dataHelical reconstruction of contracted VipA/B type six secretion tubule
Sample
  • Sample: VipA/B tubular complex in contracted state
  • Protein or peptide: VipA
  • Protein or peptide: VipB
KeywordsType Six secretion system / tail sheath structure / Vibro cholerae / VipA/B / gp18 / helical
Function / homology
Function and homology information


cellular_component / biological_process / molecular_function
Similarity search - Function
Type VI secretion system TssC-like / Type VI secretion system TssC-like / TssC1, N-terminal / TssC1, C-terminal / EvpB/VC_A0108, tail sheath N-terminal domain / EvpB/VC_A0108, tail sheath gpW/gp25-like domain / Type VI secretion system sheath protein TssB1 / Type VI secretion system sheath protein TssB1 / Type VI secretion system, VipA, VC_A0107 or Hcp2
Similarity search - Domain/homology
Type VI secretion system contractile sheath large subunit / Type VI secretion system contractile sheath small subunit
Similarity search - Component
Biological speciesVibrio cholerae O1 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsKube S / Kapitein N / Zimniak T / Herzog F / Mogk A / Wendler P
CitationJournal: Cell Rep / Year: 2014
Title: Structure of the VipA/B type VI secretion complex suggests a contraction-state-specific recycling mechanism.
Authors: Sebastian Kube / Nicole Kapitein / Tomasz Zimniak / Franz Herzog / Axel Mogk / Petra Wendler /
Abstract: The bacterial type VI secretion system is a multicomponent molecular machine directed against eukaryotic host cells and competing bacteria. An intracellular contractile tubular structure that bears ...The bacterial type VI secretion system is a multicomponent molecular machine directed against eukaryotic host cells and competing bacteria. An intracellular contractile tubular structure that bears functional homology with bacteriophage tails is pivotal for ejection of pathogenic effectors. Here, we present the 6 Å cryoelectron microscopy structure of the contracted Vibrio cholerae tubule consisting of the proteins VipA and VipB. We localized VipA and VipB in the protomer and identified structural homology between the C-terminal segment of VipB and the tail-sheath protein of T4 phages. We propose that homologous segments in VipB and T4 phages mediate tubule contraction. We show that in type VI secretion, contraction leads to exposure of the ClpV recognition motif, which is embedded in the type VI-specific four-helix-bundle N-domain of VipB. Disaggregation of the tubules by the AAA+ protein ClpV and recycling of the VipA/B subunits are thereby limited to the contracted state.
History
DepositionNov 27, 2013-
Header (metadata) releaseJan 8, 2014-
Map releaseJun 25, 2014-
UpdateJul 23, 2014-
Current statusJul 23, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2524.png

Downloads & links

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Map

FileDownload / File: emd_2524.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of contracted VipA/B type six secretion tubule
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 420 pix.
= 449.316 Å		1.07 Å/pix.
x 420 pix.
= 449.316 Å		1.07 Å/pix.
x 420 pix.
= 449.316 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0698 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-3.5601995 - 4.10327435
Average (Standard dev.)-0.02253236 (±0.22957116)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 449.316 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06981.06981.0698
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z449.316449.316449.316
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-300-299
NX/NY/NZ600600600
MAP C/R/S123
start NC/NR/NS-210-210-210
NC/NR/NS420420420
D min/max/mean-3.5604.103-0.023

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Supplemental data

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Sample components

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Entire : VipA/B tubular complex in contracted state

EntireName: VipA/B tubular complex in contracted state
Components
  • Sample: VipA/B tubular complex in contracted state
  • Protein or peptide: VipA
  • Protein or peptide: VipB

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Supramolecule #1000: VipA/B tubular complex in contracted state

SupramoleculeName: VipA/B tubular complex in contracted state / type: sample / ID: 1000 / Details: sample forms tubular complexes of varying length / Oligomeric state: VipA and VipB form heterodimer / Number unique components: 2

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Macromolecule #1: VipA

MacromoleculeName: VipA / type: protein_or_peptide / ID: 1 / Name.synonym: TssB / Oligomeric state: heterodimer with VipB in helical array / Recombinant expression: Yes
Source (natural)Organism: Vibrio cholerae O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Location in cell: cytoplasm
Molecular weightTheoretical: 18.5 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria) / Recombinant strain: XL1 Blue / Recombinant plasmid: pQE31
SequenceUniProtKB: Type VI secretion system contractile sheath small subunit
GO: biological_process, molecular_function, cellular_component
InterPro: Type VI secretion system sheath protein TssB1

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Macromolecule #2: VipB

MacromoleculeName: VipB / type: protein_or_peptide / ID: 2 / Name.synonym: TssC / Oligomeric state: heterodimer with VipA in helical array / Recombinant expression: Yes
Source (natural)Organism: Vibrio cholerae O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Location in cell: cytoplasm
Molecular weightTheoretical: 55.6 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria) / Recombinant strain: XL1 Blue / Recombinant plasmid: PQE31
SequenceUniProtKB: Type VI secretion system contractile sheath large subunit
GO: biological_process, molecular_function, cellular_component
InterPro: Type VI secretion system TssC-like

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5 / Details: 50mM Tris, 150 mM KCl, 10 mM MgCl2
GridDetails: Quantifoil R3/3 wit carbon support film, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: blot for 3.5 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJan 16, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 12271 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 145821 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsImage were processed after an adapted protocol by Clare & Orlova, 2012 (JSB)
Final reconstructionApplied symmetry - Helical parameters - Δz: 22.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 29.44 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: OTHER / Software - Name: IMAGIC, SPIDER, IHRSR
Details: dataset was symmetrized before final reconstruction as described in Clare & Orlova, 2012 (JSB)
CTF correctionDetails: each particle
Final angle assignmentDetails: theta 20 degrees, phi 60 degrees

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