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Yorodumi- PDB-5ojq: The modeled structure of of wild type extended type VI secretion ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ojq | ||||||
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Title | 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 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / T6SS / extended conformation / vibrio cholerae | ||||||
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 | ||||||
Biological species | Vibrio cholerae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Wang, J. / Brackmann, M. / Castano-Diez, D. / Kudryashev, M. / Goldie, K. / Maier, T. / Stahlberg, H. / Basler, M. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ojq.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ojq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5ojq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ojq_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5ojq_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5ojq_validation.xml.gz | 253.9 KB | Display | |
Data in CIF | 5ojq_validation.cif.gz | 442.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojq ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojq | HTTPS FTP |
-Related structure data
Related structure data | 3566MC 3563C 3564C 3567C 5mxnC 5myuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10086 (Title: Cryo EM of Type VI Secretion System VipA-N3/VipB/Hcp complex Data size: 26.2 Data #1: Unaligned multi-frame micrographs of T6SS VipA-N3/VipB/Hcp complex [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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Details | details |
-Components
#1: Protein | Mass: 18878.055 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: P72350 #2: Protein | Mass: 53504.434 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: A0A085SGI6, UniProt: Q9KN57*PLUS #3: Protein | Mass: 17099.416 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Vibrio cholerae (bacteria) / References: UniProt: A0A023PRF3, UniProt: Q9KN58*PLUS |
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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 |
-Sample preparation
Component | Name: T6SS extended sheath/tube complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Vibrio cholerae (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 23.5 ° / Axial rise/subunit: 37.8 Å / Axial symmetry: C6 |
3D reconstruction | Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10000 / Symmetry type: HELICAL |