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Open data
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Basic information
Entry | Database: PDB / ID: 5myu | ||||||||||||
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Title | VipA-N2/VipB contracted sheath of type VI secretion system | ||||||||||||
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![]() | PROTEIN TRANSPORT / Bacterial type VI secretion system / protein export | ||||||||||||
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 Similarity search - Domain/homology | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å | ||||||||||||
![]() | Wang, J. / Brackmann, B. / Castano-Diez, D. / Kudryashev, M. / Goldie, D. / Maier, T. / Stahlberg, H. / Basler, M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 895.9 KB | Display | ![]() |
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Full document | ![]() | 939.4 KB | Display | |
Data in XML | ![]() | 196.8 KB | Display | |
Data in CIF | ![]() | 313 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3567MC ![]() 3563C ![]() 3564C ![]() 3566C ![]() 5mxnC ![]() 5ojqC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 74.0 Data #1: Unaligned multi-frame micrographs of T6SS VipA-N2/VipB contracted sheath [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Number of models | 3 |
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Components
#1: Protein | Mass: 13916.752 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 48968.332 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ERS013138_01484, ERS013140_01660, ERS013165_01090, ERS013186_01572, ERS013198_01471, ERS013199_00294, ERS013200_00406, ERS013201_01395, ERS013202_00755, ERS013206_01101, ERS013207_02465 Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: Type IV secretion system sheath-tube / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 29.4 ° / Axial rise/subunit: 21.7 Å / Axial symmetry: C6 |
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7000 / Num. of class averages: 1 / Symmetry type: HELICAL |
Atomic model building | Protocol: RIGID BODY FIT |