+Open data
-Basic information
Entry | Database: PDB / ID: 3j9o | ||||||
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Title | CryoEM structure of a type VI secretion system | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / T6SS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Francisella tularensis subsp. novicida U112 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.7 Å | ||||||
Authors | Clemens, D.L. / Ge, P. / Lee, B.-Y. / Horwitz, M.A. / Zhou, Z.H. | ||||||
Citation | Journal: Cell / Year: 2015 Title: Atomic structure of T6SS reveals interlaced array essential to function. Authors: Daniel L Clemens / Peng Ge / Bai-Yu Lee / Marcus A Horwitz / Z Hong Zhou / Abstract: Type VI secretion systems (T6SSs) are newly identified contractile nanomachines that translocate effector proteins across bacterial membranes. The Francisella pathogenicity island, required for ...Type VI secretion systems (T6SSs) are newly identified contractile nanomachines that translocate effector proteins across bacterial membranes. The Francisella pathogenicity island, required for bacterial phagosome escape, intracellular replication, and virulence, was presumed to encode a T6SS-like apparatus. Here, we experimentally confirm the identity of this T6SS and, by cryo electron microscopy (cryoEM), show the structure of its post-contraction sheath at 3.7 Å resolution. We demonstrate the assembly of this T6SS by IglA/IglB and secretion of its putative effector proteins in response to environmental stimuli. The sheath has a quaternary structure with handedness opposite that of contracted sheath of T4 phage tail and is organized in an interlaced two-dimensional array by means of β sheet augmentation. By structure-based mutagenesis, we show that this interlacing is essential to secretion, phagosomal escape, and intracellular replication. Our atomic model of the T6SS will facilitate design of drugs targeting this highly prevalent secretion apparatus. | ||||||
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 | 3j9o.cif.gz | 609.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j9o.ent.gz | 508.3 KB | Display | PDB format |
PDBx/mmJSON format | 3j9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/3j9o ftp://data.pdbj.org/pub/pdb/validation_reports/j9/3j9o | HTTPS FTP |
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-Related structure data
Related structure data | 6266MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 10 / Rise per n subunits: 20.8 Å / Rotation per n subunits: -33.4 °) |
-Components
#1: Protein | Mass: 21004.932 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. novicida U112 (bacteria) References: UniProt: A0Q7I5 #2: Protein | Mass: 57942.254 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Francisella tularensis subsp. novicida U112 (bacteria) References: UniProt: A0Q7I4 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component |
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Buffer solution | Name: TBS / pH: 7.5 / Details: 20 mM Tris, 0.9% NaCl | ||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: 200 mesh Quantifoil 1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 90 K / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV) |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Mar 1, 2014 / Details: K2 Summit in Counting mode |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / Astigmatism: Software / Camera length: 0 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k) |
Image scans | Num. digital images: 1644 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: each particle | ||||||||||||
Helical symmerty | Angular rotation/subunit: 33.4 ° / Axial rise/subunit: 20.8 Å / Axial symmetry: C6 Details: One asymmetric unit contains a heterodimer of IglA/IglB | ||||||||||||
3D reconstruction | Method: RelionList of Walmart brands / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Nominal pixel size: 1 Å / Actual pixel size: 1 Å / Details: (Helical Details: Relion-based IHRSR) / Symmetry type: HELICAL | ||||||||||||
Refinement step | Cycle: LAST
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