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- EMDB-3563: Subtomogram average of type VI secretion system (T6SS) extended sheath -

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Basic information

Entry
Database: EMDB / ID: EMD-3563
TitleSubtomogram average of type VI secretion system (T6SS) extended sheathType VI secretion system
Map data
Sample
  • Complex: extended type VI secretion system (T6SS)Type VI secretion system
    • Protein or peptide: vipAVirtually imaged phased array
    • Protein or peptide: vipB
    • Protein or peptide: Hcp
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 / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp
Similarity search - Domain/homology
Type VI secretion protein / Type VI secretion system contractile sheath small subunit / Haemolysin co-regulated protein / Type VI secretion system contractile sheath large subunit / Type VI secretion system contractile sheath small subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 15.9 Å
AuthorsWang J / Castano-Diez D / Kudryashev M / 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 4, 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: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3563.png

Downloads & links

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Map

FileDownload / File: emd_3563.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 5.2 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-8.305788 - 9.339453000000001
Average (Standard dev.)-0.07257033 (±1.4854983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-49-49-49
Dimensions999899
Spacing989999
CellA: 509.59998 Å / B: 514.8 Å / C: 514.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.25.25.2
M x/y/z989999
origin x/y/z0.0000.0000.000
length x/y/z509.600514.800514.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-49-49-49
NC/NR/NS989999
D min/max/mean-8.3069.339-0.073

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Supplemental data

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Sample components

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Entire : extended type VI secretion system (T6SS)

EntireName: extended type VI secretion system (T6SS)Type VI secretion system
Components
  • Complex: extended type VI secretion system (T6SS)Type VI secretion system
    • Protein or peptide: vipAVirtually imaged phased array
    • Protein or peptide: vipB
    • Protein or peptide: Hcp

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Supramolecule #1: extended type VI secretion system (T6SS)

SupramoleculeName: extended type VI secretion system (T6SS) / type: complex / 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 TGDAQAEVAE VELPLKTLVV GDFKGHAEQT PLEERATVTV DKNNFEAVMR ESELKITATV KNKLTDDENA ELPVELNFKS LADFAPDAVA SQVPELKKLI ELREALVALK GPLGNIPAFR ERLQSLLNSE ESREKLLAEL

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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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Macromolecule #3: Hcp

MacromoleculeName: Hcp / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
SequenceString:
MPTPCYISIE GQTQGLITAG ACTADSIGDS FVEGHEDEML VQQFDHVVTV PTDPQSGQPS GQRVHKPFKF TVALNKAVPL LYNALSSGEK LKTVELKWYR TSIEGKQENF FTTKLENASI VDIHCEMPHC QDPAKSDFTQ NVTVSLSYRK ITWDHVNAGT SGSDDWRKPI EA

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 18 / Number images used: 71 / Software - Name: Dynamo
CTF correctionSoftware - Name: IMOD
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo (ver. 1.1.214) / Number subtomograms used: 5482
FSC plot (resolution estimation)

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