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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2699 | |||||||||
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Title | VipA/VipB, contractile sheath of the type VI secretion system | |||||||||
![]() | Structure of the native helical assembly isolated from Vibrio cholerae | |||||||||
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![]() | VipA / VipB / Vibrio / T6SS / cryo-EM / sheath | |||||||||
Function / homology | 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 contractile sheath large subunit / Type VI secretion system contractile sheath small subunit![]() | |||||||||
Biological species | ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Kudryashev M / Wang R / Brackmann M / Scherer S / Maier T / DiMaio F / Baker D / Stahlberg H / Egelman EH / Basler M | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 72.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.4 KB 11.4 KB | Display Display | ![]() |
Images | ![]() | 328.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3j9gMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 4.1 Data #1: Frame-averaged micrographs [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Structure of the native helical assembly isolated from Vibrio cholerae | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Native VipA/B sheath purified from Vibrio cholerae
Entire | Name: Native VipA/B sheath purified from Vibrio cholerae |
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Components |
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-Supramolecule #1000: Native VipA/B sheath purified from Vibrio cholerae
Supramolecule | Name: 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
Macromolecule | Name: VipA / type: protein_or_peptide / ID: 1 / Oligomeric state: helix built of heterodimers / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() Strain: N16961 / Location in cell: cytoplasm |
Molecular weight | Theoretical: 74 KDa |
Sequence | UniProtKB: Type VI secretion system contractile sheath large subunit |
-Macromolecule #2: VipB
Macromolecule | Name: VipB / type: protein_or_peptide / ID: 2 / Oligomeric state: helix built of heterodimers / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() Strain: N16961 / Location in cell: cytoplasm |
Molecular weight | Theoretical: 74 KDa |
Sequence | UniProtKB: Type VI secretion system contractile sheath large subunit |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | helical array |
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Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.4 / Details: PBS |
Grid | Details: Quantifoil holey carbon grids |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1.5 seconds before plunging |
Details | native polymer |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Was corrected manually at high magnification Legacy - Electron beam tilt params: 0 |
Date | Nov 15, 2013 |
Image recording | Category: 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated 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 stage | Specimen 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
Details | We used Iterative Helical Real Space Reconstruction methodology(IHRSR) |
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Final reconstruction | Applied 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 correction | Details: Ctffind for each micrograph |