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- EMDB-3567: VipA-N2/VipB contracted sheath of type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-3567
TitleVipA-N2/VipB contracted sheath of type VI secretion system
Map data
Sample
  • Organelle or cellular component: Type VI secretion system sheath
    • Protein or peptide: VipA
    • Protein or peptide: VipB
Function / homology
Function and homology information


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, VipA, VC_A0107 or Hcp2
Similarity search - Domain/homology
Type VI secretion system contractile sheath small subunit / Type VI secretion protein / Type VI secretion system contractile sheath large subunit / Type VI secretion system contractile sheath small subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWang J / Brackmann M / Castano-Diez D / Kudryashev M / Goldie K / Maier T / Stahlberg H / Basler M
CitationJournal: Nat Microbiol / Year: 2017
Title: Cryo-EM structure of the extended type VI secretion system sheath-tube complex.
Authors: Jing Wang / Maximilian Brackmann / Daniel Castaño-Díez / Mikhail Kudryashev / Kenneth N Goldie / Timm Maier / Henning Stahlberg / Marek Basler /
Abstract: The bacterial type VI secretion system (T6SS) uses contraction of a long sheath to quickly thrust a tube with associated effectors across membranes of eukaryotic and bacterial cells . Only limited ...The bacterial type VI secretion system (T6SS) uses contraction of a long sheath to quickly thrust a tube with associated effectors across membranes of eukaryotic and bacterial cells . Only limited structural information is available about the inherently unstable precontraction state of the T6SS. Here, we obtain a 3.7 Å resolution structure of a non-contractile sheath-tube complex using cryo-electron microscopy and show that it resembles the extended T6SS inside Vibrio cholerae cells. We build a pseudo-atomic model of the complete sheath-tube assembly, which provides a mechanistic understanding of coupling sheath contraction with pushing and rotating the inner tube for efficient target membrane penetration. Our data further show that sheath contraction exposes a buried recognition domain to specifically trigger the disassembly and recycling of the T6SS sheath by the cognate ATP-dependent unfoldase ClpV.
History
DepositionJan 10, 2017-
Header (metadata) releaseFeb 8, 2017-
Map releaseAug 2, 2017-
UpdateNov 8, 2017-
Current statusNov 8, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5myu
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5myu
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5myu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3567.png

Downloads & links

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Map

FileDownload / File: emd_3567.map.gz / Format: CCP4 / Size: 63.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 128 pix.
= 132.992 Å		1.04 Å/pix.
x 360 pix.
= 374.04 Å		1.04 Å/pix.
x 360 pix.
= 374.04 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: 1.039 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.05793927 - 0.097034894
Average (Standard dev.)0.0009659687 (±0.010127282)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin7676192
Dimensions360360128
Spacing360360128
CellA: 374.04 Å / B: 374.04 Å / C: 132.992 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0391.0391.039
M x/y/z360360128
origin x/y/z0.0000.0000.000
length x/y/z374.040374.040132.992
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS7676192
NC/NR/NS360360128
D min/max/mean-0.0580.0970.001

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Supplemental data

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Sample components

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Entire : Type VI secretion system sheath

EntireName: Type VI secretion system sheath
Components
  • Organelle or cellular component: Type VI secretion system sheath
    • Protein or peptide: VipA
    • Protein or peptide: VipB

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Supramolecule #1: Type VI secretion system sheath

SupramoleculeName: Type VI secretion system sheath / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: VipA

MacromoleculeName: VipA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString:
MSKEGSVAPK ERINIKYIPA TGDAQAEAEV ELPLKTLVVG DFKGHAEQTP LEERATVTVD KNNFEAVMRE SE LKITATV KNKLTDDENA ELPVELNFKS LADFAPDAVA SQVPELKKLI ELREALVALK GPLGNIPAFR ERL QSLLNS EESREKLLAE LNL

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Macromolecule #2: VipB

MacromoleculeName: VipB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString: MMSTTEKVLE RPQLAQGSLL DEIMAQTRIA PSEEGYDIAK KGVAAFIENL MGSQHSAEPV NKSLVDQMLV ELDKKISAQ MDEILHNSQF QAMESAWRGL KLFVDRTDFR ENNKVEILHV TKDELLEDFE FAPETAQSGL Y KHVYSAGY GQFGGEPVGA IIGNYAFTPS ...String:
MMSTTEKVLE RPQLAQGSLL DEIMAQTRIA PSEEGYDIAK KGVAAFIENL MGSQHSAEPV NKSLVDQMLV ELDKKISAQ MDEILHNSQF QAMESAWRGL KLFVDRTDFR ENNKVEILHV TKDELLEDFE FAPETAQSGL Y KHVYSAGY GQFGGEPVGA IIGNYAFTPS TPDMKLLQYM GALGAMAHAP FISSVGPEFF GIDSFEELPN IK DLKSTFE SPKYTKWRSL RESEDARYLG LTAPRFLLRV PYDPIENPVK SFNYAENVSA SHEHYLWGNT AFA FATRLT DSFAKYRWCP NIIGPQSGGA VEDLPVHVFE SMGALQSKIP TEVLITDRKE FELAEEGFIA LTMR KGSDN AAFFSANSIQ KPKVFPNTKE GKEAETNYKL GTQLPYMMII NRLAHYVKVL QREQIGAWKE RQDLE RELN SWIKQYVADQ ENPPADVRSR RPLRAARIEV MDVEGNPGWY QVSLSVRPHF KYMGANFELS LVGRLD QA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 186 / Average exposure time: 9.0 sec. / Average electron dose: 30.0 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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 21.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 29.4 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Details: RELION2, 3D auto-refine / Number images used: 7000
CTF correctionSoftware - Name: RELION (ver. 2)
Segment selectionNumber selected: 11620 / Software - Name: EMAN (ver. 2.1) / Software - details: e2helixboxer.py
Startup modelType of model: INSILICO MODEL / In silico model: cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-5myu:
VipA-N2/VipB contracted sheath of type VI secretion system

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