[English] 日本語
Yorodumi- PDB-7aeb: Cryo-EM structure of an extracellular contractile injection syste... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aeb | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 6-fold symmetry. | ||||||||||||
Components |
| ||||||||||||
Keywords | STRUCTURAL PROTEIN / extracellular contractile injection system | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Algoriphagus machipongonensis (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||
Authors | Xu, J. / Ericson, C. / Feldmueller, M. / Lien, Y.W. / Pilhofer, M. | ||||||||||||
Funding support | Switzerland, 3items
| ||||||||||||
Citation | 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7aeb.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7aeb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7aeb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/7aeb ftp://data.pdbj.org/pub/pdb/validation_reports/ae/7aeb | HTTPS FTP |
---|
-Related structure data
Related structure data | 11743MC 7adzC 7ae0C 7aefC 7aekC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 7 types, 42 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZabcd...
#1: Protein | Mass: 107770.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: the residues (552-end) could not be built up due to the poor map density. Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTB3 #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 built up by poly-alanine chain due to the poor map density. Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTB4 #3: Protein | Mass: 26571.104 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: The residue S169 is not found in relative map, which might be cleaved in the structure. Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTB8 #4: Protein | Mass: 15762.021 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTB5 #5: Protein | Mass: 17063.238 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC0 #6: Protein | Mass: 76319.039 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: the residues 288-320aa could not be built up in the model, with residues 430-446aa assigned with poly-alanine chain. Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC2 #7: Protein | Mass: 16375.458 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Algoriphagus machipongonensis (bacteria) / References: UniProt: A3HTC1 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry. Type: COMPLEX / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82969 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |