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- EMDB-3566: VipA-N3, non-contractile sheath of the type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-3566
TitleVipA-N3, non-contractile sheath of the type VI secretion system
Map dataPostprocessed in Relion2, average resolution is 3.7A.
Sample
  • Organelle or cellular component: vipA-N3/vipB noncontractile sheath with Hcp tube
    • Protein or peptide: Hcp
    • 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 / Type VI secretion system effector Hcp / Hcp1-like superfamily / Type VI secretion system effector, Hcp
Similarity search - Domain/homology
Type VI secretion system contractile sheath small subunit / 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)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang J / Brackmann M / Castano-Diez D / Kudryashev M / Goldie G / 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 9, 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: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5mxn
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5mxn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3566.png

Downloads & links

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Map

FileDownload / File: emd_3566.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed in Relion2, average resolution is 3.7A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 265.984 Å		1.04 Å/pix.
x 256 pix.
= 265.984 Å		1.04 Å/pix.
x 256 pix.
= 265.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.039 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.110665 - 0.16784415
Average (Standard dev.)0.0027383466 (±0.017232664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin128128128
Dimensions256256256
Spacing256256256
CellA=B=C: 265.984 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0391.0391.039
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z265.984265.984265.984
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS128128128
NC/NR/NS256256256
D min/max/mean-0.1110.1680.003

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Supplemental data

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Additional map: low-pass filtered to 5A to visualize the low-resolution...

Fileemd_3566_additional.map
Annotationlow-pass filtered to 5A to visualize the low-resolution density region of the map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : vipA-N3/vipB noncontractile sheath with Hcp tube

EntireName: vipA-N3/vipB noncontractile sheath with Hcp tube
Components
  • Organelle or cellular component: vipA-N3/vipB noncontractile sheath with Hcp tube
    • Protein or peptide: Hcp
    • Protein or peptide: VipA
    • Protein or peptide: vipB

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Supramolecule #1: vipA-N3/vipB noncontractile sheath with Hcp tube

SupramoleculeName: vipA-N3/vipB noncontractile sheath with Hcp tube / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: Hcp

MacromoleculeName: Hcp / type: protein_or_peptide / ID: 1 / 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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Macromolecule #2: VipA

MacromoleculeName: VipA / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
SequenceString:
SKEGSVAPKE RINIKYIPAT GDAQAEVAEV ELPLKTLVVG DFKGHAEQTP LEERATVTVD KNNFEAVMR ESELKITATV KNKLTDDENA ELPVELNFKS LADFAPDAVA SQVPELKKLI E LREALVAL KGPLGNIPAF RERLQSLLNS EESREKLLAE LNL

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Macromolecule #3: vipB

MacromoleculeName: vipB / type: protein_or_peptide / ID: 3 / 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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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: 37.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 23.5 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 10000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Segment selectionNumber selected: 24033 / Software - Name: e2boxer
Startup modelType of model: INSILICO MODEL
In silico model: cylinder of the same diameter of the filament
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5mxn:
Atomic model of the VipA/VipB/Hcp, the type six secretion system non-contractile sheath-tube of Vibrio cholerae from cryo-EM

PDB-5ojq:
The modeled structure of of wild type extended type VI secretion system sheath/tube complex in vibrio cholerae based on cryo-EM reconstruction of the non-contractile sheath/tube complex

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