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- PDB-7aek: Cryo-EM structure of an extracellular contractile injection syste... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aek | ||||||||||||
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Title | Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the contracted sheath shell. | ||||||||||||
![]() | Putative phage tail sheath protein FI | ||||||||||||
![]() | STRUCTURAL PROTEIN / extracellular contractile injection system | ||||||||||||
Function / homology | : / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Putative phage tail sheath protein FI![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.5 Å | ||||||||||||
![]() | Xu, J. / Ericson, C. / Feldmueller, M. / Lien, Y.W. / 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11747MC ![]() 7adzC ![]() 7ae0C ![]() 7aebC ![]() 7aefC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 76319.039 Da / Num. of mol.: 18 / Source method: isolated from a natural source Details: the residues 288-320aa are not built up in the model due to the poor map density, with residues 430-446aa assigned by poly-alanine chain. Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: The contracted sheath shell of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis. Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Helical symmerty | Angular rotation/subunit: 32.2 ° / Axial rise/subunit: 18.04 Å / Axial symmetry: C6 |
3D reconstruction | Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92922 / Symmetry type: HELICAL |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |