+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4562 | |||||||||
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Title | Subtomogram average of T6SS membrane complex TssJLM | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Escherichia coli 042 (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Kooger R / Pilhofer M | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: EMBO J / Year: 2019 Title: and high-resolution cryo-EM structure of a bacterial type VI secretion system membrane complex. Authors: Chiara Rapisarda / Yassine Cherrak / Romain Kooger / Victoria Schmidt / Riccardo Pellarin / Laureen Logger / Eric Cascales / Martin Pilhofer / Eric Durand / Rémi Fronzes / Abstract: Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is ...Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to phages. It is composed of a phage tail-like structure inserted in the bacterial cell envelope by a membrane complex (MC) comprising the TssJ, TssL and TssM proteins. We previously reported the low-resolution negative-stain electron microscopy structure of the enteroaggregative MC and proposed a rotational 5-fold symmetry with a TssJ:TssL:TssM stoichiometry of 2:2:2. Here, cryo-electron tomography analyses of the T6SS MC confirm the 5-fold symmetry and identify the regions of the structure that insert into the bacterial membranes. A high-resolution model obtained by single-particle cryo-electron microscopy highlights new features: five additional copies of TssJ, yielding a TssJ:TssL:TssM stoichiometry of 3:2:2, an 11-residue loop in TssM, protruding inside the lumen of the MC and constituting a functionally important periplasmic gate, and hinge regions. Based on these data, we propose an updated model on MC structure and dynamics during T6SS assembly and function. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4562.map.gz | 410.5 KB | EMDB map data format | |
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Header (meta data) | emd-4562-v30.xml emd-4562.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_4562.png | 91.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4562 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4562 | HTTPS FTP |
-Validation report
Summary document | emd_4562_validation.pdf.gz | 180.7 KB | Display | EMDB validaton report |
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Full document | emd_4562_full_validation.pdf.gz | 179.9 KB | Display | |
Data in XML | emd_4562_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4562 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4562 | HTTPS FTP |
-Related structure data
Related structure data | 0264C 0265C 0266C 0267C 4561C 6hs7C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4562.map.gz / Format: CCP4 / Size: 530.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 6.898 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Membrane complex of the type 6 secretion system
Entire | Name: Membrane complex of the type 6 secretion system |
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Components |
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-Supramolecule #1: Membrane complex of the type 6 secretion system
Supramolecule | Name: Membrane complex of the type 6 secretion system / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli 042 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Experimental: 1.7 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 3.0 sec. / Average electron dose: 1.3 e/Å2 Details: STA from various tomograms taken with slightly different electron dose and frame |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 23500 |
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Extraction | Number tomograms: 16 / Number images used: 28463 / Reference model: one single particle |
Final angle assignment | Type: OTHER |