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- EMDB-11745: Cryo-EM structure of an extracellular contractile injection syste... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11745 | ||||||||||||
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Title | Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 3-fold symmetry. | ||||||||||||
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Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Xu J / Ericson C / Feldmueller M / Lien YW / Pilhofer M | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 40.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
Images | ![]() | 62.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7aefMC ![]() 7adzC ![]() 7ae0C ![]() 7aebC ![]() 7aekC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : The baseplate complex of an extracellular contractile injection s...
+Supramolecule #1: The baseplate complex of an extracellular contractile injection s...
+Macromolecule #1: baseplate protein (Algo12)
+Macromolecule #2: Baseplate_J domain-containing protein
+Macromolecule #3: LysM domain-containing protein
+Macromolecule #4: Putative tail lysozyme
+Macromolecule #5: Phospholipid/glycerol acyltransferase
+Macromolecule #6: Putative phage tail sheath protein FI
+Macromolecule #7: Phage tail protein
+Macromolecule #8: inner protein (Algo6)
+Macromolecule #9: Phosphoserine phosphatase SerB
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C3 (3 fold cyclic![]() |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7aef: |