Pvc16, N-terminal / Pvc16 N-terminal domain / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube ...Pvc16, N-terminal / Pvc16 N-terminal domain / Contractile injection system tube protein, N-terminal domain / Contractile injection system tube protein / Baseplate protein J-like / Baseplate J-like protein / IraD/Gp25-like / Baseplate wedge protein gp25 / Conserved hypothetical protein CHP02241 / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / LysM domain profile. / LysM domain Similarity search - Domain/homology
Uncharacterized protein / Baseplate protein J-like domain-containing protein / Putative tail lysozyme / LysM domain-containing protein / Phospholipid/glycerol acyltransferase / Phage tail protein / Putative phage tail sheath protein FI / Uncharacterized protein / Uncharacterized protein Similarity search - Component
Biological species
Algoriphagus machipongonensis (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 4.4 Å
Journal: Nat Microbiol / Year: 2022 Title: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Authors: Jingwei Xu / Charles F Ericson / Yun-Wei Lien / Florentine U N Rutaganira / Fabian Eisenstein / Miki Feldmüller / Nicole King / Martin Pilhofer / Abstract: Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). ...Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell-cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a 'cap adaptor' located at the distal end, a 'plug' exposed to the tube lumen, and a 'cage' formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re-engineering CISs.
History
Deposition
Sep 17, 2020
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Header (metadata) release
Feb 16, 2022
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Map release
Feb 16, 2022
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Update
Mar 16, 2022
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Current status
Mar 16, 2022
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
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
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Image processing
Startup model
Type of model: NONE Details: The initial model is generated based on the orientation determined from responding baseplate complex.
Final reconstruction
Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF Details: the resolution of reconstruction reaches the Nyquist frequency of data at binning=2. However, the reconstruction map is good enough to assemble all structural models together to generate the ...Details: the resolution of reconstruction reaches the Nyquist frequency of data at binning=2. However, the reconstruction map is good enough to assemble all structural models together to generate the complete atomic model. In addition, it will cost lots of calculation resources if pursuing at the binning=1 due to huge boxsize of particles. Number images used: 52837
Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Final angle assignment
Type: MAXIMUM LIKELIHOOD
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Atomic model buiding 1
Refinement
Space: REAL / Protocol: AB INITIO MODEL
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