[English] 日本語
Yorodumi- EMDB-11744: Focused refined cryo-EM structure of an extracellular contractile... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11744 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Focused refined cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 6-fold symmetry | ||||||||||||
Map data | |||||||||||||
Sample |
| ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Algoriphagus machipongonensis (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||
Authors | Xu J / Ericson C / Feldmueller M / Lien YW / Pilhofer M | ||||||||||||
Funding support | Switzerland, 3 items
| ||||||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11744.map.gz | 47.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11744-v30.xml emd-11744.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_11744.png | 78.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11744 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11744 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11744.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : The focused refined baseplate complex of an extracellular contrac...
Entire | Name: The focused refined baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry. |
---|---|
Components |
|
-Supramolecule #1: The focused refined baseplate complex of an extracellular contrac...
Supramolecule | Name: The focused refined baseplate complex of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, applied 6-fold symmetry. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
---|---|
Source (natural) | Organism: Algoriphagus machipongonensis (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
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 |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30211 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
---|