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- EMDB-2699: VipA/VipB, contractile sheath of the type VI secretion system -

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Basic information

Entry
Database: EMDB / ID: EMD-2699
TitleVipA/VipB, contractile sheath of the type VI secretion system
Map dataStructure of the native helical assembly isolated from Vibrio cholerae
Sample
  • Sample: Native VipA/B sheath purified from Vibrio cholerae
  • Protein or peptide: VipA
  • Protein or peptide: VipB
KeywordsVipA / VipB / Vibrio / T6SS / cryo-EM / sheath
Function / homologyType 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 contractile sheath large subunit / Type VI secretion system contractile sheath small subunit
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKudryashev M / Wang R / Brackmann M / Scherer S / Maier T / DiMaio F / Baker D / Stahlberg H / Egelman EH / Basler M
CitationJournal: Cell / Year: 2015
Title: Structure of the type VI secretion system contractile sheath.
Authors: Mikhail Kudryashev / Ray Yu-Ruei Wang / Maximilian Brackmann / Sebastian Scherer / Timm Maier / David Baker / Frank DiMaio / Henning Stahlberg / Edward H Egelman / Marek Basler /
Abstract: Bacteria use rapid contraction of a long sheath of the type VI secretion system (T6SS) to deliver effectors into a target cell. Here, we present an atomic-resolution structure of a native contracted ...Bacteria use rapid contraction of a long sheath of the type VI secretion system (T6SS) to deliver effectors into a target cell. Here, we present an atomic-resolution structure of a native contracted Vibrio cholerae sheath determined by cryo-electron microscopy. The sheath subunits, composed of tightly interacting proteins VipA and VipB, assemble into a six-start helix. The helix is stabilized by a core domain assembled from four β strands donated by one VipA and two VipB molecules. The fold of inner and middle layers is conserved between T6SS and phage sheaths. However, the structure of the outer layer is distinct and suggests a mechanism of interaction of the bacterial sheath with an accessory ATPase, ClpV, that facilitates multiple rounds of effector delivery. Our results provide a mechanistic insight into assembly of contractile nanomachines that bacteria and phages use to translocate macromolecules across membranes.
History
DepositionJul 3, 2014-
Header (metadata) releaseJul 9, 2014-
Map releaseMar 4, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 120
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 120
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9g
  • Surface level: 120
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j9g
  • Surface level: 120
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2699.png

Downloads & links

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Map

FileDownload / File: emd_2699.map.gz / Format: CCP4 / Size: 268.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the native helical assembly isolated from Vibrio cholerae
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.5 Å/pix.
x 200 pix.
= 100. Å		0.5 Å/pix.
x 600 pix.
= 300. Å		0.5 Å/pix.
x 600 pix.
= 300. 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: 0.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 120.0 / Movie #1: 120
Minimum - Maximum-553.858886719999987 - 760.908996580000007
Average (Standard dev.)-99.09090424 (±111.769683839999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-99
Dimensions600600200
Spacing600600200
CellA: 300.0 Å / B: 300.0 Å / C: 100.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.50.50.5
M x/y/z600600200
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000100.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-300-300-99
NC/NR/NS600600200
D min/max/mean-553.859760.909-99.091

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Supplemental data

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Sample components

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Entire : Native VipA/B sheath purified from Vibrio cholerae

EntireName: Native VipA/B sheath purified from Vibrio cholerae
Components
  • Sample: Native VipA/B sheath purified from Vibrio cholerae
  • Protein or peptide: VipA
  • Protein or peptide: VipB

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Supramolecule #1000: Native VipA/B sheath purified from Vibrio cholerae

SupramoleculeName: Native VipA/B sheath purified from Vibrio cholerae / type: sample / ID: 1000
Oligomeric state: heterodimer of VipA and VipB assembled in a helix
Number unique components: 2

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Macromolecule #1: VipA

MacromoleculeName: VipA / type: protein_or_peptide / ID: 1 / Oligomeric state: helix built of heterodimers / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: N16961 / Location in cell: cytoplasm
Molecular weightTheoretical: 74 KDa
SequenceUniProtKB: Type VI secretion system contractile sheath large subunit

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Macromolecule #2: VipB

MacromoleculeName: VipB / type: protein_or_peptide / ID: 2 / Oligomeric state: helix built of heterodimers / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: N16961 / Location in cell: cytoplasm
Molecular weightTheoretical: 74 KDa
SequenceUniProtKB: Type VI secretion system contractile sheath large subunit

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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

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: PBS
GridDetails: Quantifoil holey carbon grids
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5 seconds before plunging
Detailsnative polymer

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Was corrected manually at high magnification
Legacy - Electron beam tilt params: 0
DateNov 15, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 72 / Average electron dose: 30 e/Å2
Details: Images were collected in dose fractionation mode and further aligned by Li and Cheng's algorithm in real time using the 2dx_automator
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 29000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt angle min: -5 / Tilt angle max: 5
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsWe used Iterative Helical Real Space Reconstruction methodology(IHRSR)
Final reconstructionApplied symmetry - Helical parameters - Δz: 21.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 29.4 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER
Software - Name: 2dx_automator, Ctffind, Helixboxer, IHRSR/Spider
Details: Resolution was detected by Resmap, it varied from 3.2 A in well ordered parts till 5 A outside of the helix.
CTF correctionDetails: Ctffind for each micrograph

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