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- PDB-7aef: 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: 7aef | ||||||||||||
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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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Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | 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. | ||||||||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 3.1 MB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 11745MC ![]() 7adzC ![]() 7ae0C ![]() 7aebC ![]() 7aekC 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
-Protein , 9 types, 48 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
#1: Protein | ![]() Mass: 107770.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: the residues (552-end) are not built up in the model due to the poor map density. Source: (natural) ![]() ![]() #2: Protein | Mass: 119379.320 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: The C-terminal part (residues 916-1012aa) is assigned with poly-alanine due to the poor map density. Source: (natural) ![]() ![]() #3: Protein | Mass: 26571.104 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: The residue S169 is not observed in the responding map density, which might be cleaved in the complex. Source: (natural) ![]() ![]() #4: Protein | Mass: 15762.021 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 17063.238 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | Mass: 76319.039 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: the residues 288-320 aa could not be built up due to the poor map density, with the residues 430-446 assigned poly-alanine chain. Source: (natural) ![]() ![]() #7: Protein | Mass: 16375.458 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | Mass: 5714.442 Da / Num. of mol.: 3 / Source method: isolated from a natural source Details: the residues (19-28) attributing to the flexible loop are not built up in the model. Source: (natural) ![]() ![]() #9: Protein | Mass: 63787.738 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 3-fold symmetry. 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![]() ![]() |
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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Symmetry | Point symmetry![]() ![]() |
3D reconstruction![]() | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82969 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |